Gas vesicles

An investigation of cyanobacteria, cyanotoxins and environmental variables in selected drinking water treatment plants in New Jersey

Harmful Algal Blooms (HAB) have the potential to impact human health primarily through their possible cyanotoxins production. While conventional water treatments can result in the removal of unlysed cyanobacterial cells and low levels of cyanotoxins, during severe HAB events, cyanotoxins can break through and can be present in the treated water due to a lack of adequate toxin treatment. The objectives of this study were to assess the HAB conditions in drinking water sources in New Jersey and investigate relationships between environmental variables and cyanobacterial communities in these drinking water sources. Source water samples were collected monthly from May to October 2019 and analyzed for phytoplankton and cyanobacterial cell densities, microcystins, cylindrospermopsin, Microcystis 16S rRNA gene, microcystin-producing mcyB gene, Raphidiopsis raciborskii-specific rpoC1 gene, and cylindrospermopsin-producing pks gene. Water quality parameters included water temperature, pH, dissolved oxygen, specific conductance, fluorescence of phycocyanin and chlorophyll, chlorophyll-a, total suspended solids, total dissolved solids, dissolved organic carbon, total nitrogen, ammonia, and total phosphorus. In addition to source waters, microcystins and cylindrospermopsin were analyzed for treated waters. The results showed all five selected New Jersey source waters had high total phosphorus concentrations that exceeded the established New Jersey Surface Water Quality Standards for lakes and rivers. Commonly found cyanobacteria were identified, such as Microcystis and Dolichospermum. Site E was the site most susceptible to HABs with significantly greater HAB variables, such as extracted phycocyanin, fluorescence of phycocyanin, cyanobacterial cell density, microcystins, and Microcystis 16S rRNA gene. All treated waters were undetected with microcystins, indicating treatment processes were effective at removing toxins from source waters. Results also showed that phycocyanin values had a significantly positive relationship with microcystin concentration, copies of Microcystis 16S rRNA and microcystin-producing mcyB genes, suggesting these values can be used as a proxy for HAB monitoring. This study suggests that drinking water sources in New Jersey are vulnerable to forthcoming HAB. Monitoring and management of source waters is crucial to help safeguard public health.

Dependence of evolution of Cyanobacteria superiority on temperature and nutrient use efficiency in a meso-eutrophic plateau lake

Algal blooms in lakes have been a challenging environmental issue globally under the dual influence of human activity and climate change. Considerable progress has been made in the study of phytoplankton dynamics in lakes; The long-term in situ evolution of dominant bloom-forming cyanobacteria in meso-eutrophic plateau lakes, however, lacks systematic research. Here, the monthly parameters from 12 sampling sites during the period of 1997-2022 were utilized to investigate the underlying mechanisms driving the superiority of bloom-forming cyanobacteria in Erhai, a representative meso-eutrophic plateau lake. The findings indicate that global warming will intensify the risk of cynaobacteria blooms, prolong Microcystis blooms in autumn to winter or even into the following year, and increase the superiority of filamentous Planktothrix and Cylindrospermum in summer and autumn. High RUETN (1.52 Biomass/TN, 0.95-3.04 times higher than other species) under N limitation (TN < 0.5 mg/L, TN/TP < 22.6) in the meso-eutrophic Lake Erhai facilitates the superiority of Dolichospermum. High RUETP (43.8 Biomass/TP, 2.1-10.2 times higher than others) in TP of 0.03-0.05 mg/L promotes the superiority of Planktothrix and Cylindrospermum. We provided a novel insight into the formation of Planktothrix and Cylindrospermum superiority in meso-eutrophic plateau lake with low TP (0.005-0.07 mg/L), which is mainly influenced by warming, high RUETP and their vertical migration characteristics. Therefore, we posit that although the obvious improvement of lake water quality is not directly proportional to the control efficacy of cyanobacterial blooms, the evolutionary shift in cyanobacteria population structure from Microcystis, which thrives under high nitrogen and phosphorus conditions, to filamentous cyanobacteria adapted to low nitrogen and phosphorus levels may serve as a significant indicator of water quality amelioration. Therefore, we suggest that the risk of filamentous cyanobacteria blooms in the meso-eutrophic plateau lake should be given attention, particularly in light of improving water quality and global warming, to ensure drinking water safety.

Satellite mapping reveals phytoplankton biomass's spatio-temporal dynamics and responses to environmental factors in a eutrophic inland lake

Chlorophyll a (Chla) concentration can be used as an indicator of algal biomass, and the accumulation of algal biomass in water column is essential for the emergence of surface blooms. By using Moderate Resolution Imaging Spectrometer (MODIS) data, a machine learning algorithm was previously developed to assess algal biomass within the euphotic depth (Beu). Here, a long-term Beu dataset of Lake Taihu from 2003 to 2020 was generated to examine its spatio-temporal dynamics, sensitivity to environmental factors, and variations in comparison to the surface algal bloom area. During this period, the daily Beu (total Beu within the whole lake) exhibited temporal fluctuations between 40 and 90 t Chla, with an annual average of 63.32 ± 5.23 t Chla. Notably, it reached its highest levels in 2007 (72.34 t Chla) and 2017 (73.57 t Chla). Moreover, it demonstrated a clear increasing trend of 0.197 t Chla/y from 2003 to 2007, followed by a slight decrease of 0.247 t Chla/y after 2017. Seasonal variation showed a bimodal annual cycle, characterized by a minor peak in March ∼ April and a major peak in July ∼ September. Spatially, the average pixel-based Beu (total Beu of a unit water column) ranged from 21.17 to 49.85 mg Chla, with high values predominantly distributed in the northwest region and low values in the central region. The sensitivity of Beu to environmental factors varies depending on regions and time scales. Temperature has a significant impact on monthly variation (65.73%), while the level of nutrient concentrations influences annual variation (55.06%). Wind speed, temperature, and hydrodynamic conditions collectively influence the spatial distribution of Beu throughout the entire lake. Algal bloom biomass can capture trend changes in two mutant years as well as bimodal phenological changes compared to surface algal bloom area. This study can provide a basis for scientific evaluation of water environment and a reference for monitoring algal biomass in other similar eutrophic lakes.

The use of coagulant and natural soil to control cyanobacterial blooms in a tropical reservoir

Cyanobacterial blooms have been a growing problem in water bodies and attracted attention from researcher and water companies worldwide. Different treatment methods have been researched and applied either inside water treatment plants or directly into reservoirs. We tested a combination of coagulants, polyaluminium chloride (PAC) and iron(III) chloride (FeCl3), and ballasts, luvisol (LUV) and planosol (PLAN), known as the 'Floc and Sink' technique, to remove positively buoyant cyanobacteria from a tropical reservoir water. Response Surface Methodology (RSM) based on Central Composite Design (CCD) was used to optimize the two reaction variables - coagulant dosage (x1) and ballast dosage (x2) to remove the response variables: chlorophyll-a, turbidity, true color, and organic matter. Results showed that the combination of LUV with PAC effectively reduced the concentration of the response variables, while PLAN was ineffective in removing cyanobacteria when combined to PAC or FeCl3. Furthermore, FeCl3 presented poorer floc formation and lower removal efficiency compared to PAC. This study may contribute to the theoretical and practical knowledge of the algal biomass removal for mitigating eutrophication trough different dosages of coagulants and ballasts.

Rapid flotation of Microcystis wesenbergii mediated by high light exposure: implications for surface scum formation and cyanobacterial species succession

Increasing occurrences of Microcystis surface scum have been observed in the context of global climate change and the increase in anthropogenic pollution, causing deteriorating water quality in aquatic ecosystems. Previous studies on scum formation mainly focus on the buoyancy-driven floating process of larger Microcystis colonies, neglecting other potential mechanisms. To study the non-buoyancy-driven rapid flotation of Microcystis, we here investigate the floating processes of two strains of single-cell species (Microcystis aeruginosa and Microcystis wesenbergii), which are typically buoyant, under light conditions (150 μmol photons s-1 m-2). Our results showed that M. wesenbergii exhibited fast upward migration and formed surface scum within 4 hours, while M. aeruginosa did not form visible scum throughout the experiments. To further explore the underlying mechanism of these processes, we compared the dissolved oxygen (DO), extracellular polymeric substance (EPS) content, and colony size of Microcystis in different treatments. We found supersaturated DO and the formation of micro-bubbles (50-200 µm in diameter) in M. wesenbergii treatments. M. aeruginosa produces bubbles in small quantities and small sizes. Additionally, M. wesenbergii produced more EPS and tended to aggregate into larger colonies. M. wesenbergii had much more derived-soluble extracellular proteins and polysaccharides compared to M. aeruginosa. At the same time, M. wesenbergii contains abundant functional groups, which was beneficial to the formation of agglomerates. The surface scum observed in M. wesenbergii is likely due to micro-bubbles attaching to the surface of cell aggregates or becoming trapped within the colony. Our study reveals a species-specific mechanism for the rapid floatation of Microcystis, providing novel insights into surface scum formation as well as succession of cyanobacterial species.

Phase transition of GvpU regulates gas vesicle clustering in bacteria

Gas vesicles (GVs) are microbial protein organelles that support cellular buoyancy. GV engineering has multiple applications, including reporter gene imaging, acoustic control and payload delivery. GVs often cluster into a honeycomb pattern to minimize occupancy of the cytosol. The underlying molecular mechanism and the influence on cellular physiology remain unknown. Using genetic, biochemical and imaging approaches, here we identify GvpU from Priestia megaterium as a protein that regulates GV clustering in vitro and upon expression in Escherichia coli. GvpU binds to the C-terminal tail of the core GV shell protein and undergoes a phase transition to form clusters in subsaturated solution. These properties of GvpU tune GV clustering and directly modulate bacterial fitness. GV variants can be designed with controllable sensitivity to GvpU-mediated clustering, enabling design of genetically tunable biosensors. Our findings elucidate the molecular mechanisms and functional roles of GV clustering, enabling its programmability for biomedical applications.

Directed Evolution of Acoustic Reporter Genes Using High-Throughput Acoustic Screening

A major challenge in the fields of biological imaging and synthetic biology is noninvasively visualizing the functions of natural and engineered cells inside opaque samples such as living animals. One promising technology that addresses this limitation is ultrasound (US), with its penetration depth of several cm and spatial resolution on the order of 100 µm. 1 Within the past decade, reporter genes for US have been introduced 2,3 and engineered 4,5 to link cellular functions to US signals via heterologous expression in commensal bacteria and mammalian cells. These acoustic reporter genes (ARGs) represent a novel class of genetically encoded US contrast agent, and are based on air-filled protein nanostructures called gas vesicles (GVs). 6 Just as the discovery of fluorescent proteins was followed by the improvement and diversification of their optical properties through directed evolution, here we describe the evolution of GVs as acoustic reporters. To accomplish this task, we establish high-throughput, semi-automated acoustic screening of ARGs in bacterial cultures and use it to screen mutant libraries for variants with increased nonlinear US scattering. Starting with scanning site saturation libraries for two homologs of the primary GV structural protein, GvpA/B, two rounds of evolution resulted in GV variants with 5- and 14-fold stronger acoustic signals than the parent proteins. We anticipate that this and similar approaches will help high-throughput protein engineering play as large a role in the development of acoustic biomolecules as it has for their fluorescent counterparts.

50-nm Gas-Filled Protein Nanostructures to Enable the Access of Lymphatic Cells by Ultrasound Technologies

Ultrasound imaging and ultrasound-mediated gene and drug delivery are rapidly advancing diagnostic and therapeutic methods; however, their use is often limited by the need for microbubbles, which cannot transverse many biological barriers due to their large size. Here, the authors introduce 50-nm gas-filled protein nanostructures derived from genetically engineered gas vesicles(GVs) that are referred to as 50 nmGVs. These diamond-shaped nanostructures have hydrodynamic diameters smaller than commercially available 50-nm gold nanoparticles and are, to the authors' knowledge, the smallest stable, free-floating bubbles made to date. 50 nmGVs can be produced in bacteria, purified through centrifugation, and remain stable for months. Interstitially injected 50 nmGVs can extravasate into lymphatic tissues and gain access to critical immune cell populations, and electron microscopy images of lymph node tissues reveal their subcellular location in antigen-presenting cells adjacent to lymphocytes. The authors anticipate that 50 nmGVs can substantially broaden the range of cells accessible to current ultrasound technologies and may generate applications beyond biomedicine as ultrasmall stable gas-filled nanomaterials.

Genetic Modulation of Biosynthetic Gas Vesicles for Ultrasound Imaging

Gas vesicles (GVs) from microorganisms are genetically air-filled protein nanostructures, and serve as a new class of nanoscale contrast agents for ultrasound imaging. Recently, the genetically encoded GV gene clusters have been heterologously expressed in Escherichia coli, allowing these genetically engineered bacteria to be visualized in vivo in a real-time manner by ultrasound. However, most of the GV genes remained functionally uncharacterized, which makes it difficult to regulate and modify GVs for broad medical applications. Here, the impact of GV proteins on GV formation is systematically investigated. The results first uncovered that the deletions of GvpR or GvpU resulted in the formation of a larger proportion of small, biconical GVs compared to the full-length construct, and the deletion of GvpT resulted in a larger portion of large GVs. Meanwhile, the combination of gene deletions has resulted in several genotypes of ultrasmall GVs that span from 50 to 20 nm. Furthermore, the results showed that E. coli carrying the ΔGvpCRTU mutant can produce strong ultrasound contrast signals in mouse liver. In conclusion, the study provides new insights into the roles of GV proteins in GV formation and produce ultrasmall GVs with a wide range of in vivo research.

Sonogenetics for Monitoring and Modulating Biomolecular Function by Ultrasound

Ultrasound technology, synergistically harnessed with genetic engineering and chemistry concepts, has started to open the gateway to the remarkable realm of sonogenetics-a pioneering paradigm for remotely orchestrating cellular functions at the molecular level. This fusion not only enables precisely targeted imaging and therapeutic interventions, but also advances our comprehension of mechanobiology to unparalleled depths. Sonogenetic tools harness mechanical force within small tissue volumes while preserving the integrity of the surrounding physiological environment, reaching depths of up to tens of centimeters with high spatiotemporal precision. These capabilities circumvent the inherent physical limitations of alternative in vivo control methods such as optogenetics and magnetogenetics. In this review, we first discuss mechanosensitive ion channels, the most commonly utilized sonogenetic mediators, in both mammalian and non-mammalian systems. Subsequently, we provide a comprehensive overview of state-of-the-art sonogenetic approaches that leverage thermal or mechanical features of ultrasonic waves. Additionally, we explore strategies centered around the design of mechanochemically reactive macromolecular systems. Furthermore, we delve into the realm of ultrasound imaging of biomolecular function, encompassing the utilization of gas vesicles and acoustic reporter genes. Finally, we shed light on limitations and challenges of sonogenetics and present a perspective on the future of this promising technology.

Nanobubble-actuated ultrasound neuromodulation for selectively shaping behavior in mice

Ultrasound is an acoustic wave which can noninvasively penetrate the skull to deep brain regions, enabling neuromodulation. However, conventional ultrasound's spatial resolution is diffraction-limited and low-precision. Here, we report acoustic nanobubble-mediated ultrasound stimulation capable of localizing ultrasound's effects to only the desired brain region in male mice. By varying the delivery site of nanobubbles, ultrasound could activate specific regions of the mouse motor cortex, evoking EMG signaling and limb movement, and could also, separately, activate one of two nearby deep brain regions to elicit distinct behaviors (freezing or rotation). Sonicated neurons displayed reversible, low-latency calcium responses and increased c-Fos expression in the sub-millimeter-scale region with nanobubbles present. Ultrasound stimulation of the relevant region also modified depression-like behavior in a mouse model. We also provide evidence of a role for mechanosensitive ion channels. Altogether, our treatment scheme allows spatially-targetable, repeatable and temporally-precise activation of deep brain circuits for neuromodulation without needing genetic modification.

What makes a cyanobacterial bloom disappear? A review of the abiotic and biotic cyanobacterial bloom loss factors

Cyanobacterial blooms present substantial challenges to managers and threaten ecological and public health. Although the majority of cyanobacterial bloom research and management focuses on factors that control bloom initiation, duration, toxicity, and geographical extent, relatively little research focuses on the role of loss processes in blooms and how these processes are regulated. Here, we define a loss process in terms of population dynamics as any process that removes cells from a population, thereby decelerating or reducing the development and extent of blooms. We review abiotic (e.g., hydraulic flushing and oxidative stress/UV light) and biotic factors (e.g., allelopathic compounds, infections, grazing, and resting cells/programmed cell death) known to govern bloom loss. We found that the dominant loss processes depend on several system specific factors including cyanobacterial genera-specific traits, in situ physicochemical conditions, and the microbial, phytoplankton, and consumer community composition. We also address loss processes in the context of bloom management and discuss perspectives and challenges in predicting how a changing climate may directly and indirectly affect loss processes on blooms. A deeper understanding of bloom loss processes and their underlying mechanisms may help to mitigate the negative consequences of cyanobacterial blooms and improve current management strategies.

Structural biology of microbial gas vesicles: historical milestones and current knowledge

Gas vesicles mediate buoyancy-based motility in aquatic bacteria and archaea and are the only protein-based structures known to enclose a gas-filled volume. Their unique physicochemical properties and ingenious architecture rank them among the most intriguing macromolecular assemblies characterised to date. This review covers the 60-year journey in quest for a high-resolution structural model of gas vesicles, first highlighting significant strides made in establishing the detailed ultrastructure of gas vesicles through transmission electron microscopy, X-ray fibre diffraction, atomic force microscopy, and NMR spectroscopy. We then survey the recent progress in cryogenic electron microscopy studies of gas vesicles, which eventually led to a comprehensive atomic model of the mature assembly. Synthesising insight from these structures, we examine possible mechanisms of gas vesicle biogenesis and growth, presenting a testable model to guide future experimental work. We conclude by discussing future directions in the structural biology of gas vesicles, particularly considering advancements in AI-driven structure prediction.

Hyperpolarized Xenon-129 Chemical Exchange Saturation Transfer (HyperCEST) Molecular Imaging: Achievements and Future Challenges

Molecular magnetic resonance imaging (MRI) is an emerging field that is set to revolutionize our perspective of disease diagnosis, treatment efficacy monitoring, and precision medicine in full concordance with personalized medicine. A wide range of hyperpolarized (HP) 129Xe biosensors have been recently developed, demonstrating their potential applications in molecular settings, and achieving notable success within in vitro studies. The favorable nuclear magnetic resonance properties of 129Xe, coupled with its non-toxic nature, high solubility in biological tissues, and capacity to dissolve in blood and diffuse across membranes, highlight its superior role for applications in molecular MRI settings. The incorporation of reporters that combine signal enhancement from both hyperpolarized 129Xe and chemical exchange saturation transfer holds the potential to address the primary limitation of low sensitivity observed in conventional MRI. This review provides a summary of the various applications of HP 129Xe biosensors developed over the last decade, specifically highlighting their use in MRI. Moreover, this paper addresses the evolution of in vivo applications of HP 129Xe, discussing its potential transition into clinical settings.

Gas Vesicle-Blood Interactions Enhance Ultrasound Imaging Contrast

Gas vesicles (GVs) are genetically encoded, air-filled protein nanostructures of broad interest for biomedical research and clinical applications, acting as imaging and therapeutic agents for ultrasound, magnetic resonance, and optical techniques. However, the biomedical applications of GVs as systemically injectable nanomaterials have been hindered by a lack of understanding of GVs' interactions with blood components, which can significantly impact in vivo behavior. Here, we investigate the dynamics of GVs in the bloodstream using a combination of ultrasound and optical imaging, surface functionalization, flow cytometry, and mass spectrometry. We find that erythrocytes and serum proteins bind to GVs and shape their acoustic response, circulation time, and immunogenicity. We show that by modifying the GV surface we can alter these interactions and thereby modify GVs' in vivo performance. These results provide critical insights for the development of GVs as agents for nanomedicine.

Encapsulins: Nanotechnology's future in a shell

Encapsulins, virus capsid-like bacterial nanocompartments have emerged as promising tools in medicine, imaging, and material sciences. Recent work has shown that these protein-bound icosahedral 'organelles' possess distinct properties that make them exceptionally usable for nanotechnology applications. A key factor contributing to their appeal is their ability to self-assemble, coupled with their capacity to encapsulate a wide range of cargos. Their genetic manipulability, stability, biocompatibility, and nano-size further enhance their utility, offering outstanding possibilities for practical biotechnology applications. In particular, their amenability to engineering has led to their extensive modification, including the packaging of non-native cargos and the utilization of the shell surface for displaying immunogenic or targeting proteins and peptides. This inherent versatility, combined with the ease of expressing encapsulins in heterologous hosts, promises to provide broad usability. Although mostly not yet commercialized, encapsulins have started to demonstrate their vast potential for biotechnology, from drug delivery to biofuel production and the synthesis of valuable inorganic materials. In this review, we will initially discuss the structure, function and diversity of encapsulins, which form the basis for these emerging applications, before reviewing ongoing practical uses and highlighting promising applications in medicine, engineering and environmental sciences.

Impact of critical eddy diffusivity on seasonal bloom dynamics of Phytoplankton in a global set of aquatic environments

The intensity of eddy diffusivity and the spatial average of water velocity at the depths of the water column in oceans and lakes play a fundamental role in phytoplankton production and phytoplankton and zooplankton biomass, and community composition. The critical depth and intensity of turbulent mixing within the water column profoundly affect phytoplankton biomass, which depends on the sinking characteristic of planktonic algal species. We propose an Nutrient-Phytoplankton-Zooplankton (NPZ) model in 3D space with light and nutrient-limited growth in a micro-scale ecological study. To incorporate micro-scale observation of phytoplankton intermittency in bloom mechanism in stationary as well as oceanic turbulent flows, a moment closure method has been applied in this study. Experimental observations imply that an increase in turbulence is sometimes ecologically advantageous for non-motile planktonic algae. How do we ensure whether there will be a bloom cycle or whether there can be any bloom at all when the existing phytoplankton group is buoyant, heavier, motile, or non-motile? To address these questions, we have explored the effects of critical depth, the intensity of eddy diffusivity, spatial average of water velocity, on the concentration as well as horizontal and vertical distribution of phytoplankton and zooplankton biomass using a mathematical model and moment closure technique. We quantify a critical threshold value of eddy diffusivity and the spatial average of water velocity and observe the corresponding changes in the phytoplankton bloom dynamics. Our results highlight the importance of eddy diffusivity and the spatial average of water velocity on seasonal bloom dynamics and also mimic different real-life bloom scenarios in Mikawa Bay (Japan), Tokyo Bay (Japan), Arakawa River (Japan), the Baltic Sea, the North Atlantic Ocean, Gulf Alaska, the North Arabian Sea, the Cantabrian Sea, Lake Nieuwe Meer (Netherlands) and several shallower lakes.

Living Material with Temperature-Dependent Light Absorption

Engineered living materials (ELMs) exhibit desirable characteristics of the living component, including growth and repair, and responsiveness to external stimuli. Escherichia coli (E. coli) are a promising constituent of ELMs because they are very tractable to genetic engineering, produce heterologous proteins readily, and grow exponentially. However, seasonal variation in ambient temperature presents a challenge in deploying ELMs outside of a laboratory environment because E. coli growth rate is impaired both below and above 37 °C. Here, a genetic circuit is developed that controls the expression of a light-absorptive chromophore in response to changes in temperature. It is demonstrated that at temperatures below 36 °C, the engineered E. coli increase in pigmentation, causing an increase in sample temperature and growth rate above non-pigmented counterparts in a model planar ELM. On the other hand, at above 36 °C, they decrease in pigmentation, protecting the growth compared to bacteria with temperature-independent high pigmentation. Integrating the temperature-responsive circuit into an ELM has the potential to improve living material performance by optimizing growth and protein production in the face of seasonal temperature changes.

Nanovesicular-Mediated Intranasal Drug Therapy for Neurodegenerative Disease

Numerous neurodegenerative conditions, such as Alzheimer's, Huntington's, Parkinson's, amyotrophic lateral sclerosis, and glioblastoma multiform are now becoming significant concerns of global health. Formulation-related issues, physiological and anatomical barriers, post-administration obstacles, physical challenges, regulatory limitations, environmental hurdles, and health and safety issues have all hindered successful delivery and effective outcomes despite a variety of treatment options. In the current review, we covered the intranasal route, an alternative strategic route targeting brain for improved delivery across the BBB. The trans-nasal pathway is non-invasive, directing therapeutics directly towards brain, circumventing the barrier and reducing peripheral exposure. The delivery of nanosized vesicles loaded with drugs was also covered in the review. Nanovesicle systems are organised in concentric bilayered lipid membranes separated with aqueous layers. These carriers surmount the disadvantages posed by intranasal delivery of rapid mucociliary clearance and enzymatic degradation, and enhance retention of drug to reach the site of target. In conclusion, the review covers in-depth conclusions on numerous aspects of formulation of drug-loaded vesicular system delivery across BBB, current marketed nasal devices, significant jeopardies, potential therapeutic aids, and current advancements followed by future perspectives.

Biogenic Imaging Contrast Agents

Imaging contrast agents are widely investigated in preclinical and clinical studies, among which biogenic imaging contrast agents (BICAs) are developing rapidly and playing an increasingly important role in biomedical research ranging from subcellular level to individual level. The unique properties of BICAs, including expression by cells as reporters and specific genetic modification, facilitate various in vitro and in vivo studies, such as quantification of gene expression, observation of protein interactions, visualization of cellular proliferation, monitoring of metabolism, and detection of dysfunctions. Furthermore, in human body, BICAs are remarkably helpful for disease diagnosis when the dysregulation of these agents occurs and can be detected through imaging techniques. There are various BICAs matched with a set of imaging techniques, including fluorescent proteins for fluorescence imaging, gas vesicles for ultrasound imaging, and ferritin for magnetic resonance imaging. In addition, bimodal and multimodal imaging can be realized through combining the functions of different BICAs, which helps overcome the limitations of monomodal imaging. In this review, the focus is on the properties, mechanisms, applications, and future directions of BICAs.

Extremophiles: the species that evolve and survive under hostile conditions

Extremophiles possess unique cellular and molecular mechanisms to assist, tolerate, and sustain their lives in extreme habitats. These habitats are dominated by one or more extreme physical or chemical parameters that shape existing microbial communities and their cellular and genomic features. The diversity of extremophiles reflects a long list of adaptations over millions of years. Growing research on extremophiles has considerably uncovered and increased our understanding of life and its limits on our planet. Many extremophiles have been greatly explored for their application in various industrial processes. In this review, we focused on the characteristics that microorganisms have acquired to optimally thrive in extreme environments. We have discussed cellular and molecular mechanisms involved in stability at respective extreme conditions like thermophiles, psychrophiles, acidophiles, barophiles, etc., which highlight evolutionary aspects and the significance of extremophiles for the benefit of mankind.

Ultrasound Molecular Imaging of Bladder Cancer via Extradomain B Fibronectin-Targeted Biosynthetic GVs

Purpose

Ultrasound molecular imaging (UMI) has proven promising to diagnose the onset and progression of diseases such as angiogenesis, inflammation, and thrombosis. However, microbubble-based acoustic probes are confined to intravascular targets due to their relatively large particle size, greatly reducing the application value of UMI, especially for extravascular targets. Extradomain B fibronectin (ED-B FN) is an important glycoprotein associated with tumor genesis and development and highly expressed in many types of tumors. Here, we developed a gas vesicles (GVs)-based nanoscale acoustic probe (ZD2-GVs) through conjugating ZD2 peptides which can specially target to ED-B FN to the biosynthetic GVs.

Materials and Methods

ED-B FN expression was evaluated in normal liver and tumor tissues with immunofluorescence and Western blot. ZD2-GVs were prepared by conjugating ZD2 to the surface of GVs by amide reaction. The inverted microscope was used to analyze the targeted binding capacity of ZD2-GVs to MB49 cells (bladder cancer cell line). The contrast-enhanced imaging features of GVs, non-targeted control GVs (CTR-GVs), and targeted GVs (ZD2-GVs) were compared in three MB49 tumor mice. The penetration ability of ZD2-GVs in tumor tissues was assessed by fluorescence immunohistochemistry. The biosafety of GVs was evaluated by CCK8, blood biochemistry, and HE staining.

Results

Strong ED-B FN expression was observed in tumor tissues while little expression in normal liver tissues. The resulting ZD2-GVs had only 267.73 ± 2.86 nm particle size and exhibited excellent binding capability to the MB49 tumor cells. The in vivo UMI experiments showed that ZD2-GVs produced stronger and longer retention in the BC tumors than that of the non-targeted CTR-GVs and GVs. Fluorescence immunohistochemistry confirmed that ZD2-GVs could penetrate the tumor vascular into the interstitial space of the tumors. Biosafety analysis revealed there was no significant cytotoxicity to these tested mice.

Conclusion

Thus, ZD2-GVs can function as a potential UMI probe for the early diagnosis of bladder cancer.

Gas vesicle-blood interactions enhance ultrasound imaging contrast

Gas vesicles (GVs) are genetically encoded, air-filled protein nanostructures of broad interest for biomedical research and clinical applications, acting as imaging and therapeutic agents for ultrasound, magnetic resonance, and optical techniques. However, the biomedical applications of GVs as a systemically injectable nanomaterial have been hindered by a lack of understanding of GVs' interactions with blood components, which can significantly impact in vivo performance. Here, we investigate the dynamics of GVs in the bloodstream using a combination of ultrasound and optical imaging, surface functionalization, flow cytometry, and mass spectrometry. We find that erythrocytes and serum proteins bind to GVs and shape their acoustic response, circulation time, and immunogenicity. We show that by modifying the GV surface, we can alter these interactions and thereby modify GVs' in vivo performance. These results provide critical insights for the development of GVs as agents for nanomedicine.

50-nm gas-filled protein nanostructures to enable the access of lymphatic cells by ultrasound technologies

Ultrasound imaging and ultrasound-mediated gene and drug delivery are rapidly advancing diagnostic and therapeutic methods; however, their use is often limited by the need of microbubbles, which cannot transverse many biological barriers due to their large size. Here we introduce 50-nm gas-filled protein nanostructures derived from genetically engineered gas vesicles that we referred to as 50nm GVs. These diamond-shaped nanostructures have hydrodynamic diameters smaller than commercially available 50-nm gold nanoparticles and are, to our knowledge, the smallest stable, free-floating bubbles made to date. 50nm GVs can be produced in bacteria, purified through centrifugation, and remain stable for months. Interstitially injected 50nm GVs can extravasate into lymphatic tissues and gain access to critical immune cell populations, and electron microscopy images of lymph node tissues reveal their subcellular location in antigen-presenting cells adjacent to lymphocytes. We anticipate that 50nm GVs can substantially broaden the range of cells accessible to current ultrasound technologies and may generate applications beyond biomedicine as ultrasmall stable gas-filled nanomaterials.

Truly tiny acoustic biomolecules for ultrasound imaging and therapy

Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography has been challenging due to the size and stability constraints of conventional bubble-based agents. Here we describe bicones, truly tiny acoustic contrast agents based on gas vesicles, a unique class of air-filled protein nanostructures naturally produced in buoyant microbes. We show that these sub-80 nm particles can be effectively detected both in vitro and in vivo, infiltrate tumors via leaky vasculature, deliver potent mechanical effects through ultrasound-induced inertial cavitation, and are easily engineered for molecular targeting, prolonged circulation time, and payload conjugation.

Effect of light-mediated variations of colony morphology on the buoyancy regulation of Microcystis colonies

Light is an important driver of algal growth and for the formation of surface blooms. Long-term buoyancy maintenance of Microcystis colonies is crucial for their aggregation at the water surface and the following algal bloom development. However, the effect of light-mediated variations of colony morphology on the buoyancy regulation of Microcystis colonies remains unclear. In this study, growth parameters, colony morphology and floatation/sinking performance of Microcystis colonies were determined to explore how variations in colony morphology influence the buoyancy of colonies under different light conditions. We quantified colony compactness through the cell volume to colony volume ratio (VR) and found different responses of colony size and VR under different light intensities. Microcystis colonies with higher VR could stay longer at the water surface under low light conditions, which was beneficial for the long-term growth and buoyancy maintenance. However, increased colony size and decreased compactness were observed at a later growth stage under relatively higher light intensity (i.e., >108 µmol photons m^-2 s^-1). Interestingly, we found a counterintuitive negative correlation between colony size and buoyancy of Microcystis under high light intensity. Additionally, we found that the influence of colony morphology on buoyancy was stronger at high light intensity. These results indicate that light could regulate the buoyancy via colonial morphology and that the role of colony morphology in buoyancy regulation needs to be accounted for in further studies under variable environmental conditions.

Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET

Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a β sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.

Swimming of Buoyant Bacteria in Quiescent Medium and Shear Flows

Gravity has an unavoidable effect on all living organisms inhabiting fluidic surroundings. To investigate the spatial distribution of bacteria in quiescent fluids and their rheotactic behavior in shear flows under buoyancy, we adjust the buoyant force to regulate bacterial swimming in a microfluidic channel. It is found that swimming bacteria of Escherichia coli exhibit an obvious vertical separation when exposed to a medium with high density and gradually gather close to the up wall within minutes. The bacterial population presents a net upward number flux, which enhances the trapping of motile bacteria onto the up surface as a result of buoyancy force apart from the hydrodynamic and kinematic interactions in quiescent fluids. When flow is imposed into the channel, the buoyancy effect is however significantly suppressed. Additionally, the drift velocity perpendicular to the buoyancy vector as a result of chirality-induced transverse swimming decreases with buoyancy force. However, this transverse drift capability is recovered after excluding the intrinsic swimming motility in a quiescent medium. Failing to escape from the trapping as a result of buoyant force allows for a facile separation of bacteria along the vertical direction. The findings also offer a controllable way to redisperse and homogenize the bacteria distribution close to walls by imposing a weak shear flow.

Engineered Living Materials For Sustainability

Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.

Cryo-EM structure of gas vesicles for buoyancy-controlled motility

Gas vesicles are gas-filled nanocompartments that allow a diverse group of bacteria and archaea to control their buoyancy. The molecular basis of their properties and assembly remains unclear. Here, we report the 3.2 Å cryo-EM structure of the gas vesicle shell made from the structural protein GvpA that self-assembles into hollow helical cylinders closed off by cone-shaped tips. Two helical half shells connect through a characteristic arrangement of GvpA monomers, suggesting a mechanism of gas vesicle biogenesis. The fold of GvpA features a corrugated wall structure typical for force-bearing thin-walled cylinders. Small pores enable gas molecules to diffuse across the shell, while the exceptionally hydrophobic interior surface effectively repels water. Comparative structural analysis confirms the evolutionary conservation of gas vesicle assemblies and demonstrates molecular features of shell reinforcement by GvpC. Our findings will further research into gas vesicle biology and facilitate molecular engineering of gas vesicles for ultrasound imaging.

Microbiology and Climate Change: a Transdisciplinary Imperative

Climate change is a complex problem involving nonlinearities and feedback that operate across scales. No single discipline or way of thinking can effectively address the climate crisis. Teams of natural scientists, social scientists, engineers, economists, and policymakers must work together to understand, predict, and mitigate the rapidly accelerating impacts of climate change. Transdisciplinary approaches are urgently needed to address the role that microorganisms play in climate change. Here, we demonstrate with case studies how diverse teams and perspectives provide climate-change insight related to the range expansion of emerging fungal pathogens, technological solutions for harmful cyanobacterial blooms, and the prediction of disease-causing microorganisms and their vector populations using massive networks of monitoring stations. To serve as valuable members of a transdisciplinary climate research team, microbiologists must reach beyond the boundaries of their immediate areas of scientific expertise and engage in efforts to build open-minded teams aimed at scalable technologies and adoptable policies.

Cyanobacterial membrane dynamics in the light of eukaryotic principles

Intracellular compartmentalization is a hallmark of eukaryotic cells. Dynamic membrane remodeling, involving membrane fission/fusion events, clearly is crucial for cell viability and function, as well as membrane stabilization and/or repair, e.g., during or after injury. In recent decades, several proteins involved in membrane stabilization and/or dynamic membrane remodeling have been identified and described in eukaryotes. Yet, while typically not having a cellular organization as complex as eukaryotes, also bacteria can contain extra internal membrane systems besides the cytoplasmic membranes (CMs). Thus, also in bacteria mechanisms must have evolved to stabilize membranes and/or trigger dynamic membrane remodeling processes. In fact, in recent years proteins, which were initially defined being eukaryotic inventions, have been recognized also in bacteria, and likely these proteins shape membranes also in these organisms. One example of a complex prokaryotic inner membrane system is the thylakoid membrane (TM) of cyanobacteria, which contains the complexes of the photosynthesis light reaction. Cyanobacteria are evolutionary closely related to chloroplasts, and extensive remodeling of the internal membrane systems has been observed in chloroplasts and cyanobacteria during membrane biogenesis and/or at changing light conditions. We here discuss common principles guiding eukaryotic and prokaryotic membrane dynamics and the proteins involved, with a special focus on the dynamics of the cyanobacterial TMs and CMs.

Biomolecular actuators for genetically selective acoustic manipulation of cells

The ability to physically manipulate specific cells is critical for the fields of biomedicine, synthetic biology, and living materials. Ultrasound has the ability to manipulate cells with high spatiotemporal precision via acoustic radiation force (ARF). However, because most cells have similar acoustic properties, this capability is disconnected from cellular genetic programs. Here, we show that gas vesicles (GVs)-a unique class of gas-filled protein nanostructures-can serve as genetically encodable actuators for selective acoustic manipulation. Because of their lower density and higher compressibility relative to water, GVs experience strong ARF with opposite polarity to most other materials. When expressed inside cells, GVs invert the cells' acoustic contrast and amplify the magnitude of their ARF, allowing the cells to be selectively manipulated with sound waves based on their genotype. GVs provide a direct link between gene expression and acoustomechanical actuation, opening a paradigm for selective cellular control in a broad range of contexts.

The buckling-condensation mechanism driving gas vesicle collapse

Gas vesicles (GVs) are proteinaceous cylindrical shells found within bacteria or archea growing in aqueous environments and are composed primarily of two proteins, gas vesicle protein A and C (GvpA and GvpC). GVs exhibit strong performance as next-generation ultrasound contrast agents due to their gas-filled interior, tunable collapse pressure, stability in vivo and functionalizable exterior. However, the exact mechanism leading to GV collapse remains inconclusive, which leads to difficulty in predicting collapse pressures for different species of GVs and in extending favorable nonlinear response regimes. Here, we propose a two stage mechanism leading to GV loss of echogenicity and rupture under hydrostatic pressure: elastic buckling of the cylindrical shell coupled with condensation driven weakening of the GV membrane. Our goal is to therefore test whether the final fracture of the GV membrane occurs by the interplay of both mechanisms or purely through buckling failure as previously believed. To do so, we (1) compare the theoretical condensation and buckling pressures with that for experimental GV collapse and (2) describe how condensation can lead to plastic buckling failure. GV shell properties that are necessary input to this theoretical description, such as the elastic moduli and wettability of GvpA, are determined using molecular dynamics simulations of a novel structural model of GvpA that better represents the hydrophobic core. For GVs that are not reinforced by GvpC, this analytical framework shows that the experimentally observed pressures resulting in loss of echogenicity coincide with both the elastic buckling and condensation pressure regimes. We also found that the stress strain curve for GvpA wetted on both the interior and exterior exhibits a loss of mechanical stability compared to GvpA only wetted on the exterior by the bulk solution. We identify a pressure vs. vesicle size regime where condensation can occur prior to buckling, which may preclude nonlinear shell buckling responses in contrast imaging.

Ancient DNA reveals potentially toxic cyanobacteria increasing with climate change

Cyanobacterial blooms in freshwater systems are a global threat to human and aquatic ecosystem health, exhibiting particularly harmful effects when toxin-producing taxa are present. While climatic change and nutrient over-enrichment control the global expansion of total cyanobacterial blooms, it remains unknown to what extent this expansion reflected cyanobacterial assemblage due to the scarcity of long-term monitoring data. Here we use high-throughput sequencing of sedimentary DNA to track ∼100 years of changes in cyanobacterial community in hyper-eutrophic Lake Taihu, China's third largest freshwater lake and the key water source for ∼30 million people. A steady increase in the abundance of Microcystis (as potential toxin producers) during the past thirty years was correlated with increasing temperatures and declining wind speeds, but not with temporal trends in lakewater nutrient concentrations, highlighting recent climate effects on potentially increasing toxin-producing taxa. The socio-environmental repercussions of these findings are worrisome as continued anthropogenic climate change may counteract nutrient amelioration efforts in this critical freshwater resource.

Rapid in situ assessment of high-resolution spatial and temporal distribution of cyanobacterial blooms using fishery echosounder

Cyanobacterial blooms are increasing in frequency, magnitude, and duration globally because of enhanced eutrophication and climate change. Thus, comprehensive investigation and systematic monitoring of the spatial and temporal distribution of cyanobacteria in aquatic environments are urgently needed to better understand bloom development and complex interactions within a dynamic environment. Various methods have been used to investigate the distribution of cyanobacteria, however, none of them can provide high-resolution data for the three-dimensional spatial structure of the bloom and its dynamics in real time. In the present study, we investigated the applicability of a high-frequency (200 kHz) fishery echosounder, a type widely used in fisheries acoustics, to detect and estimate the cyanobacterial genus Microcystis bloom distribution and biomass in a shallow lake (Sulejów Reservoir, Poland). Verification of the usefulness of in situ acoustic quantification of bloom-forming cyanobacteria was based on a comparison of acoustic estimates of cyanobacterial biomass with the ground truth-that is, fluorometric measurements and chlorophyll a concentrations. We compared the acoustic estimates with other methods for continuous measurements along 10 predetermined parallel transects and point samples at 14 stations situated on the transects. In vertical hydroacoustic measurements at night, we observed that cyanobacterial biomass was highest in the uppermost layer and diminished continuously with depth. For both horizontal and vertical continuous measurements, we found significant positive correlations between acoustic and fluorometric estimates of cyanobacterial biomass. The traditional point samples measurements, however, did not agree equally well with the acoustic estimates, especially for vertical beam. We argue that the point measurements have more stochastic character and less adequately describe dynamic changes in the cyanobacteria distribution than continuous acoustic estimates. More studies are required to explore the cyanobacteria distribution patterns under different biological, physical, and meteorological conditions.

Environmental factors affecting akinete germination and resting cell awakening of two cyanobacteria

Globally, cyanobacteria frequently cause blooms that outcompete other species in the waterbody, affecting the diversity, decreasing water exchange rates, and promoting eutrophication that leads to excessive algal growth. Here, Dolichospermum circinale (akinetes) and Microcystic aeruginosa (resting cells), were isolated from the sediment in the Uiam Dam in the North Han River and near Ugok Bridge in the Nakdong River, respectively. The morphology, germination process and rates, and growth was evaluated in different environmental conditions. D. cercinalis germination began on day two of culturing, with maximum cell growth observed on day ten. In contrast, M. aeruginosa exhibited daily increase in cell density and colony size, with notable density increase on day six. Next, different environmental conditions were assessed. Akinetes exhibited high germination rates at low light intensity (5-30 µmol/m²/s), whereas resting cells exhibited high growth rates at high light intensity (50-100 µmol/m²/s). Furthermore, both cell types exhibited optimum germination and growth in media containing N and P at 20-30° at a pH of 7-9. Our study reveals the optimum conditions for the germination and growth of cyanobacterial akinetes and resting cells isolated from river sediment, respectively, and will assist in predicting cyanobacterial blooms for appropriate management.

Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors and tumor-homing bacteria

Ultrasound allows imaging at a much greater depth than optical methods, but existing genetically encoded acoustic reporters for in vivo cellular imaging have been limited by poor sensitivity, specificity and in vivo expression. Here we describe two acoustic reporter genes (ARGs)-one for use in bacteria and one for use in mammalian cells-identified through a phylogenetic screen of candidate gas vesicle gene clusters from diverse bacteria and archaea that provide stronger ultrasound contrast, produce non-linear signals distinguishable from background tissue and have stable long-term expression. Compared to their first-generation counterparts, these improved bacterial and mammalian ARGs produce 9-fold and 38-fold stronger non-linear contrast, respectively. Using these new ARGs, we non-invasively imaged in situ tumor colonization and gene expression in tumor-homing therapeutic bacteria, tracked the progression of tumor gene expression and growth in a mouse model of breast cancer, and performed gene-expression-guided needle biopsies of a genetically mosaic tumor, demonstrating non-invasive access to dynamic biological processes at centimeter depth.

Ultrasound nanotheranostics: Toward precision medicine

Ultrasound (US) is a mechanical wave that can penetrate biological tissues and trigger complex bioeffects. The mechanisms of US in different diagnosis and treatment are different, and the functional application of commercial US is also expanding. In particular, recent developments in nanotechnology have led to a wider use of US in precision medicine. In this review, we focus on US in combination with versatile micro and nanoparticles (NPs)/nanovesicles for tumor theranostics. We first introduce US-assisted drug delivery as a stimulus-responsive approach that spatiotemporally regulates the deposit of nanomedicines in target tissues. Multiple functionalized NPs and their US-regulated drug-release curves are analyzed in detail. Moreover, as a typical representative of US therapy, sonodynamic antitumor strategy is attracting researchers' attention. The collaborative efficiency and mechanisms of US and various nano-sensitizers such as nano-porphyrins and organic/inorganic nanosized sensitizers are outlined in this paper. A series of physicochemical processes during ultrasonic cavitation and NPs activation are also discussed. Finally, the new applications of US and diagnostic NPs in tumor-monitoring and image-guided combined therapy are summarized. Diagnostic NPs contain substances with imaging properties that enhance US contrast and photoacoustic imaging. The development of such high-resolution, low-background US-based imaging methods has contributed to modern precision medicine. It is expected that the integration of non-invasive US and nanotechnology will lead to significant breakthroughs in future clinical applications.

Comparative genomic insights into habitat adaptation of coral-associated Prosthecochloris

Green sulfur bacteria (GSB) are a distinct group of anoxygenic phototrophic bacteria that are found in many ecological niches. Prosthecochloris, a marine representative genus of GSB, was found to be dominant in some coral skeletons. However, how coral-associated Prosthecochloris (CAP) adapts to diurnal changing microenvironments in coral skeletons is still poorly understood. In this study, three Prosthecochloris genomes were obtained through enrichment culture from the skeleton of the stony coral Galaxea fascicularis. These divergent three genomes belonged to Prosthecochloris marina and two genomes were circular. Comparative genomic analysis showed that between the CAP and non-CAP clades, CAP genomes possess specialized metabolic capacities (CO oxidation, CO₂ hydration and sulfur oxidation), gas vesicles (vertical migration in coral skeletons), and cbb ₃-type cytochrome c oxidases (oxygen tolerance and gene regulation) to adapt to the microenvironments of coral skeletons. Within the CAP clade, variable polysaccharide synthesis gene clusters and phage defense systems may endow bacteria with differential cell surface structures and phage susceptibility, driving strain-level evolution. Furthermore, mobile genetic elements (MGEs) or evidence of horizontal gene transfer (HGT) were found in most of the genomic loci containing the above genes, suggesting that MGEs play an important role in the evolutionary diversification between CAP and non-CAP strains and within CAP clade strains. Our results provide insight into the adaptive strategy and population evolution of endolithic Prosthecochloris strains in coral skeletons.

Low Salt Influences Archaellum-Based Motility, Glycerol Metabolism, and Gas Vesicles Biogenesis in Halobacterium salinarum

Halobacterium salinarum NRC-1 is an extremophile that grows optimally at 4.3 M NaCl concentration. In spite of being an established model microorganism for the archaea domain, direct comparisons between its proteome and transcriptome during osmotic stress are still not available. Through RNA-seq-based transcriptomics, we compared a low salt (2.6 M NaCl) stress condition with 4.3 M of NaCl and found 283 differentially expressed loci. The more commonly found classes of genes were: ABC-type transporters and transcription factors. Similarities, and most importantly, differences between our findings and previously published datasets in similar experimental conditions are discussed. We validated three important biological processes differentially expressed: gas vesicles production (due to down-regulation of gvpA1b, gvpC1b, gvpN1b, and gvpO1b); archaellum formation (due to down-regulation of arlI, arlB1, arlB2, and arlB3); and glycerol metabolism (due to up-regulation of glpA1, glpB, and glpC). Direct comparison between transcriptomics and proteomics showed 58% agreement between mRNA and protein level changes, pointing to post-transcriptional regulation candidates. From those genes, we highlight rpl15e, encoding for the 50S ribosomal protein L15e, for which we hypothesize an ionic strength-dependent conformational change that guides post-transcriptional processing of its mRNA and, thus, possible salt-dependent regulation of the translation machinery.

Remote sensing to detect harmful algal blooms in inland waterbodies

Harmful algal blooms (HABs) are an issue of concern for water management worldwide. As such, effective monitoring strategies of HAB spatio-temporal variability in waterbodies are needed. Remote sensing has become an increasingly important tool for HAB detection and monitoring in large lakes. However, accurate HAB detection in small-medium waterbodies via satellite data remains a challenge. Current barriers include the waterbody size, the limited freely available high resolution satellite data, and the lack of field calibration data. To test the applicability of remote sensing for detecting HABs in small-medium waterbodies, three satellites (Planetscope, Sentinel-2 and Landsat-8) were used to understand how spatial resolution, the availability of spectral bands, and the waterbody size itself effect HAB detection skill. Different algorithms and a non-parametric method, Self-Organizing Map (SOM), were tested. Curvature Around Red and NIR minus Red had the best HAB detection skill of the 20 existing algorithms that were tested. Landsat 8 and Sentinel 2 were the best satellites for HAB detection in small to medium waterbodies. The most critical attribute for detecting HABs were the available satellite bands, which determine the detection algorithms that can be used. Importantly, algorithm performance was mostly unrelated to waterbody size. However, there remain some barriers in utilizing satellite data for HAB detection, including algae dynamics, macrophyte cover within the waterbody, weather effects, and the correction models for satellite data. Moreover, it is important to consider the match time between satellite overpass and sampling activities for calibration. Given these challenges, integrating regular sampling activities and remote sensing is recommended for monitoring and managing small-medium waterbodies.

Mechanisms and models of movement of protocells and bacteria in the early stages of evolution

A review of the physicochemical models of the movement of protocells and bacteria was performed. The mechanisms of gliding and movement based on flagella are considered. Based on the models, the average speed of movement of protocells and bacteria was calculated. A physicochemical model of bacterial gliding was constructed. The efficiency of the process of converting the energy of ATP into the energy of motion is estimated. A review of models of movement with the help of flagella was performed. A model has been constructed for converting ATP energy into proton and sodium motive forces, which, in turn, are converted into energy of rotor rotation. The problem of the accuracy of operation of nanomachines, on the basis of which the directed movement of bacteria occurs, is discussed. The considered models can be applied to create nanomotors for medical purposes.

Geometric effects in gas vesicle buckling under ultrasound

Acoustic reporter genes based on gas vesicles (GVs) have enabled the use of ultrasound to noninvasively visualize cellular function in vivo. The specific detection of GV signals relative to background acoustic scattering in tissues is facilitated by nonlinear ultrasound imaging techniques taking advantage of the sonomechanical buckling of GVs. However, the effect of geometry on the buckling behavior of GVs under exposure to ultrasound has not been studied. To understand such geometric effects, we developed computational models of GVs of various lengths and diameters and used finite element simulations to predict their threshold buckling pressures and postbuckling deformations. We demonstrated that the GV diameter has an inverse cubic relation to the threshold buckling pressure, whereas length has no substantial effect. To complement these simulations, we experimentally probed the effect of geometry on the mechanical properties of GVs and the corresponding nonlinear ultrasound signals. The results of these experiments corroborate our computational predictions. This study provides fundamental insights into how geometry affects the sonomechanical properties of GVs, which, in turn, can inform further engineering of these nanostructures for high-contrast, nonlinear ultrasound imaging.

Magneto-Mechanical Approach in Biomedicine: Benefits, Challenges, and Future Perspectives

The magneto-mechanical approach is a powerful technique used in many different applications in biomedicine, including remote control enzyme activity, cell receptors, cancer-selective treatments, mechanically-activated drug releases, etc. This approach is based on the use of a combination of magnetic nanoparticles and external magnetic fields that have led to the movement of such nanoparticles with torques and forces (enough to change the conformation of biomolecules or even break weak chemical bonds). However, despite many theoretical and experimental works on this topic, it is difficult to predict the magneto-mechanical effects in each particular case, while the important results are scattered and often cannot be translated to other experiments. The main reason is that the magneto-mechanical effect is extremely sensitive to changes in any parameter of magnetic nanoparticles and the environment and changes in the parameters of the applied magnetic field. Thus, in this review, we (1) summarize and propose a simplified theoretical explanation of the main factors affecting the efficiency of the magneto-mechanical approach; (2) discuss the nature of the MNP-mediated mechanical forces and their order of magnitude; (3) show some of the main applications of the magneto-mechanical approach in the control over the properties of biological systems.

Recent Advances in the Study of Gas Vesicle Proteins and Application of Gas Vesicles in Biomedical Research

The formation of gas vesicles has been investigated in bacteria and haloarchaea for more than 50 years. These air-filled nanostructures allow cells to stay at a certain height optimal for growth in their watery environment. Several gvp genes are involved and have been studied in Halobacterium salinarum, cyanobacteria, Bacillus megaterium, and Serratia sp. ATCC39006 in more detail. GvpA and GvpC form the gas vesicle shell, and additional Gvp are required as minor structural proteins, chaperones, an ATP-hydrolyzing enzyme, or as gene regulators. We analyzed the Gvp proteins of Hbt. salinarum with respect to their protein–protein interactions, and developed a model for the formation of these nanostructures. Gas vesicles are also used in biomedical research. Since they scatter waves and produce ultrasound contrast, they could serve as novel contrast agent for ultrasound or magnetic resonance imaging. Additionally, gas vesicles were engineered as acoustic biosensors to determine enzyme activities in cells. These applications are based on modifications of the surface protein GvpC that alter the mechanical properties of the gas vesicles. In addition, gas vesicles have been decorated with GvpC proteins fused to peptides of bacterial or viral pathogens and are used as tools for vaccine development.

Reporter Genes for Brain Imaging Using MRI, SPECT and PET

The use of molecular imaging technologies for brain imaging can not only play an important supporting role in disease diagnosis and treatment but can also be used to deeply study brain functions. Recently, with the support of reporter gene technology, optical imaging has achieved a breakthrough in brain function studies at the molecular level. Reporter gene technology based on traditional clinical imaging modalities is also expanding. By benefiting from the deeper imaging depths and wider imaging ranges now possible, these methods have led to breakthroughs in preclinical and clinical research. This article focuses on the applications of magnetic resonance imaging (MRI), single-photon emission computed tomography (SPECT), and positron emission tomography (PET) reporter gene technologies for use in brain imaging. The tracking of cell therapies and gene therapies is the most successful and widely used application of these techniques. Meanwhile, breakthroughs have been achieved in the research and development of reporter genes and their imaging probe pairs with respect to brain function research. This paper introduces the imaging principles and classifications of the reporter gene technologies of these imaging modalities, lists the relevant brain imaging applications, reviews their characteristics, and discusses the opportunities and challenges faced by clinical imaging modalities based on reporter gene technology. The conclusion is provided in the last section.

Production and transformation of organic matter driven by algal blooms in a shallow lake: Role of sediments

The generation of organic matter (OM) occurs synchronously with phytoplankton growth. Characterization of the generated particulate and dissolved OM during algal blooms in eutrophic lakes is crucial for better understanding the carbon cycle but remains limited. We speculate that sediments play a critical role in the biogeochemical transformation of OM derived from algal blooms in shallow lakes. In this study, changes in OM quantity and quality and the concentrations of biogenic elements (nutrients and metals) during algal blooms, were studied in situ in a shallow eutrophic lake (Lake Chaohu, China). Two enclosure treatments in the presence and absence of sediments were compared, and the cause-effect relationships among sediment, nutrients, metals, phytoplankton, particulate OM (POM), and dissolved OM (DOM) were revealed by a partial least square-path model (PLS-PM). The results showed that the changes in nutrients and metals concentrations over time were consistent with that of chlorophyll a (Chl a), and at the end of the treatment, the concentrations of Chl a, nutrients, and metals in Treatment S (with sediments) were approximately 3-5 times of those in Treatment N (without sediments). The high concentration of Chl a in Treatment S resulted in a high quantity of POM, which showed low molecular weight, low humification, and was enriched in protein-like components (∼ 70%). For DOM, the quantity increased after the decrease in POM, and DOM quality showed a significantly higher abundance of humic-like components and a higher molecular weight than POM did. The PLS-PM results showed that the significant positive effects of sediment on nutrients, metals, phytoplankton, POM, and DOM were 0.28, 0.37, 0.28, 0.25, and 0.25, respectively, suggesting that sediment had an important role in the biogeochemical cycles of these substances. The significant negative relationship between POM and DOM (-0.62) and the distinct difference in POM and DOM quality implied the efficient transformation of the freshly generated OM to those with a higher molecular weight, higher humification, and potentially refractory. Our results depicted the quick biogeochemical transformation of nutrients, metals, and the potential formation of refractory organic carbon in water column, as driven by the couple of the algae pump with the microbial carbon pump.

Taphonomy of microorganisms and microbial microtextures at sulfidic hydrothermal vents: A case study from the Roman Ruins black smokers, Eastern Manus Basin

Biological activity at deep-sea hydrothermal chimneys is driven by chemotrophic microorganisms that metabolize chemicals from the venting high-temperature fluids. Understanding taphonomy and microbial microtextures in such environments is a necessity for micropaleontological and palaeoecological research. This study examines fossilized microorganisms and related microtextures in a recent black smoker from the Roman Ruins hydrothermal vent site, Eastern Manus Basin offshore of Papua New Guinea. Whereas the center of the examined sulfide chimney is dominated by high-temperature mineralogy (chalcopyrite and dendritic sphalerite), filamentous and coccoidal biomorphs occur in an outer, warm zone of mixing between hydrothermal fluids and seawater, which is indicated by their occurrence within colloform and botryoidal pyrite of barite-pyrite coprecipitates. Both morphotypes can be interpreted as thermophilic microorganisms based on their occurrence in a high-temperature habitat. Their separate (non-commensal) occurrence hints at sensitivities to microenvironmental conditions, which is expectable for strong temperature, pH, and redox gradients at the walls of deep-sea hydrothermal chimneys. Whereas both morphotypes experienced mild thermal overprint, taphonomic differences exist: (i) spaces left by cells in filamentous fossils are predominately filled by silica, whereas inter/extracellular features (crosswalls/septae and outer sheaths) are pyritized; (ii) coccoidal fossils show both silica- and pyrite-infilled interiors, and generally better preservation of cell walls. These different manifestations presumably relate to an interplay between microenvironmental and biological factors, potentially contrasting metabolisms, and differences in cell wall chemistries of distinct bacteria and/or archaea. A further hypothesis is that the coccoidal features represent biofilm-forming organisms, whose organic matter derivates contributed to the formation of intimately associated wavy and wrinkly carbonaceous laminations that are at least locally distinguishable from the texture of the surrounding pyrite. Hence, the presented data provide evidence that microtextures of microbiota from hydrothermal systems can have a similar significance for palaeobiological research as those from sedimentary environments.