Biology subjects

Ueki, T.

Publications and source records attributed to Ueki, T..

16 recordsLinked to original sources

bioRxiv2025

The sympathoadrenal contribution to inferior vena cava formation

Vascular development is fundamental during embryogenesis. Although the molecular and cellular mechanisms of vascular formation have been extensively studied, the developmental basis common to anatomical variations in major veins remains poorly understood1-4. In particular, the renal segment of the inferior vena cava (IVC) exhibits marked anatomical variability, and these structural differences often affect the safety of retroperitoneal surgeries5,6. Here we show that the renal segment of the IVC in mouse embryos does not arise from the subcardinal vein (SubCV), as classically proposed7, but instead forms from a vascular plexus in the para-aortic ridge (PAR) closely associated with developing sympathetic and adrenal tissues. Three-dimensional imaging with molecular markers revealed the vascular plexus in PAR arises independently of the SubCV and develops in Zuckerkandl organ and adrenal gland primordia. Moreover, genetic models demonstrated that the development of the sympathetic and adrenal tissues contributes to the organization and remodeling of this vascular network. This sympathoadrenal contribution contrasts with the classical mesonephros-centric model and explains the consistent IVC structures observed even in the absence of renal development. Our findings suggest a mammal-specific mode of IVC formation driven by the emergence of dominant sympathetic paraganglia and reduced reliance on mesonephric filtration. This revised developmental framework provides insight into the evolutionary divergence of venous anatomy and may help interpret clinically significant vascular variations during abdominal surgery.

developmental biology↗

bioRxiv2024

Incorporating Microbial Pilin-Based Nanowires into a Water-Stable Electronic Polymer Composite

Electrically conductive protein nanowires (e-PNs), microbially produced from a pilin monomer, are a novel, sustainable electronic material that can be genetically tailored for specific functions. e-PNs, expressed with Escherichia coli grown on the biodiesel byproduct glycerol, and mixed with polyvinyl butyral yielded a transparent, electrically conductive water-stable composite.Composite conductivity was adjusted by modifying the e-PN concentration or incorporating e-PNs genetically tuned for different conductivities. Electronic devices in which composites were the sensor component differentially responded to dissolved ammonia over a wide concentration range (1{micro}M-1M). Genetically modifying e-PNs to display an ammonia-binding peptide on their outer surface increased the sensor response to ammonia 10-fold. These results, coupled with the flexibility to design peptides for specific binding of diverse analytes, demonstrate that sustainably produced e-PNs offer the possibility of incorporating multiple sensor components, each specifically designed to detect different analytes with high sensitivity and selectivity, within one small sensor device.

bioengineering↗

bioRxiv2024

Medium Composition Affects Microbial Corrosion Rates

Desulfovibrio vulgaris and Desulfovibrio ferrophilus were previously proposed to have distinct iron corrosion mechanisms because D. ferrophilus corroded faster. However, the chloride concentration in the D. ferrophilus marine medium was much higher than in the D. vulgaris freshwater medium. D. vulgaris corrosion rates accelerated with increasing chloride and were faster than D. ferrophilus in the same marine medium. Differences in D. ferrophilus corrosion rates in two different media with the same chloride concentration suggested that minor differences in other medium constituents also impact on microbial corrosion. These results demonstrate the importance of considering medium composition in microbial corrosion studies.

microbiology↗

bioRxiv2024

Elucidating Microbial Iron Corrosion Mechanisms with a Hydrogenase-Deficient Strain of Desulfovibrio vulgaris

Sulfate-reducing microorganisms extensively contribute to the corrosion of ferrous metal infrastructure. There is substantial debate over their corrosion mechanisms. We investigated Fe0 corrosion with Desulfovibrio vulgaris, the sulfate reducer most often employed in corrosion studies. Cultures were grown with both lactate and Fe0 as potential electron donors to replicate the common environmental condition in which organic substrates help fuel the growth of corrosive microbes. Fe0 was corroded in cultures of a D. vulgaris hydrogenase-deficient mutant with the 1:1 correspondence between Fe0 loss and H2 accumulation expected for Fe0 oxidation coupled to H+ reduction to H2. This result and the extent of sulfate reduction indicated that D. vulgaris was not capable of direct Fe0-to-microbe electron transfer even though it was provided with a supplementary energy source in the presence of abundant ferrous sulfide. Corrosion in the hydrogenase-deficient mutant cultures was greater than in sterile controls, demonstrating the H2 removal was not necessary for the enhanced corrosion observed in the presence of microbes. The parental H2-consuming strain corroded more Fe0 than the mutant strain, which could be attributed to H2 oxidation coupled to sulfate reduction producing sulfide that further stimulated Fe0 oxidation. The results suggest that H2 consumption is not necessary for microbially enhanced corrosion, but H2 oxidation can indirectly promote corrosion by increasing sulfide generation from sulfate reduction. The finding that, D. vulgaris was incapable of direct electron uptake from Fe0 reaffirms that direct metal-to-microbe electron transfer has yet to be rigorously described in sulfate-reducing microbes. Impact StatementThe economic impact of microbial corrosion of iron-containing metals is substantial. A better understanding of how microbes accelerate corrosion is expected to lead to the development of methods to prevent corrosion. The results presented here refute the suggestion, frequently made in the microbiology literature, that microbial H2 uptake stimulates Fe0 corrosion. Also refuted, are previous claims that Desulfovibrio vulgaris is capable of directly extracting electrons from Fe0. The results are consistent with the concept that sulfide produced by sulfate-reducers promotes Fe0 oxidation with the production of H2. The results illustrate that appropriate mutants can provide rigor to corrosion mechanism studies.

microbiology↗

bioRxiv2023

Antibody Complementarity-Determining Region Sequence Design using AlphaFold2 and Binding Affinity Prediction Model

Affinity maturation in the immune response is limited in terms of affinity gain, and natural antibodies often do not have the binding affinity required for therapeutic applications. Therefore, improving the binding affinity of antibodies is essential for developing antibody-based therapeutics. Designing antibodies using experimental methods is expensive in terms of cost and time owing to the large range of complementarity-determining regions to be explored. Recently, computational methods have been developed as low-cost and fast means of designing and redesigning antibodies. This study evaluated the design performance of AlphaFold2 and the binder hallucination, which can predict protein 3D structures with high accuracy even without experimental antibodies, by redesigning antibody sequences to improve the binding affinity of existing antigen-antibody complexes. Therefore, antibody sequences with higher affinity can be designed for antigen-antibody complexes not included in the training data of AlphaFold2, indicating that the proposed method may be effective as an antibody design method.

bioinformatics↗

bioRxiv2023

The defects of the hippocampal ripples and theta rhythm in depression, and the effects of physical exercise on their amelioration.

Accumulated evidence demonstrate that environmental stress affects the hippocampus, functioning in cognition and sociality, and causes various depressive symptoms. In addition, recent findings showed that environmental stress influenced the hippocampal activity correlated with neuroinflammation, and impaired the hippocampal sharp wave ripples (SWRs), pattens of spike sequences, and the theta rhythms, a strong oscillation observed in the hippocampus. The involvement of the electrophysiological alterations in the etiology of depression has not been appreciated especially in the hippocampus. Furthermore, the pathological markers associated with such alterations have not been identified. In the present study, therefore, the impairment of the SWRs and the theta rhythms in the hippocampus of the restraint stress-induced depression model of mice was analyzed. In the model mice the hippocampal SWRs and theta rhythms were impaired in depression, while physical exercise significantly reverted them. As previously reported, chronic stress induced inflammation in the affected hippocampus in parallel with defects of adult neurogenesis, on the other hand physical exercise ameliorated those pathological conditions of the bran in depression. In conclusion, this study demonstrated the implications of impairment of the hippocampal SWRs and theta rhythms in the etiology of depression and their usefulness as diagnostic markers of depression.

neuroscience↗

bioRxiv2022

H2 is a Major Intermediate in Desulfovibrio vulgaris Corrosion of Iron

Desulfovibrio vulgaris has been the primary pure culture sulfate reducer for developing microbial corrosion concepts. Multiple mechanisms for how it accepts electrons from Fe0 have been proposed. We investigated Fe0 oxidation with a mutant of D. vulgaris in which hydrogenase genes were deleted. The hydrogenase mutant grew as well as the parental strain with lactate as the electron donor, but unlike the parental strain was not able to grow on H2. The parental strain reduced sulfate with Fe0 as the sole electron donor, but the hydrogenase mutant did not. H2 accumulated over time in Fe0 cultures of the hydrogenase mutant and sterile controls, but not in parental strain cultures. Sulfide stimulated H2 production in uninoculated controls apparently by both reacting with Fe0 to generate H2 and facilitating electron transfer from Fe0 to H+. Parental strain supernatants did not accelerate H2 production from Fe0, ruling out a role for extracellular hydrogenases. Previously proposed electron transfer between Fe0 and D. vulgaris via soluble electron shuttles was not evident. The hydrogenase mutant did not reduce sulfate in the presence of Fe0 and either riboflavin or anthraquinone-2,6-disulfonate and these potential electron shuttles did not stimulate parental strain sulfate reduction with Fe0 as the electron donor. The results demonstrate that D. vulgaris primarily accepts electrons from Fe0 via H2 as an intermediary electron carrier. These findings clarify the interpretation of previous D. vulgaris corrosion studies and suggest that H2-mediated electron transfer is an important mechanism for iron corrosion under sulfate-reducing conditions. ImportanceMicrobial corrosion of iron in the presence of sulfate-reducing microorganisms is economically significant. There is substantial debate over how microbes accelerate iron corrosion. Tools for genetic manipulation have only been developed for a few Fe(III)-reducing and methanogenic microorganisms known to corrode iron and in each case those microbes were found to accept electrons from Fe0 via direct electron transfer. However, iron corrosion is often most intense in the presence of sulfate-reducing microbes. The finding that Desulfovibrio vulgaris relies on H2 to shuttle electrons between Fe0 and cells revives the concept, developed in some of the earliest studies on microbial corrosion, that sulfate reducers consumption of H2 is a major microbial corrosion mechanism. The results further emphasize that direct Fe0-to-microbe electron transfer has yet to be rigorously demonstrated in sulfate-reducing microbes.

microbiology↗

bioRxiv2022

Microbial nanowires with genetically modified peptide ligands to sustainably fabricate electronic sensing devices

Nanowires have substantial potential as the sensor component in electronic sensing devices. However, surface functionalization of traditional nanowire and nanotube materials with short peptides that increase sensor selectivity and sensitivity requires complex chemistries with toxic reagents. In contrast, microorganisms can assemble pilin monomers into protein nanowires with intrinsic conductivity from renewable feedstocks, yielding an electronic material that is robust and stable in applications, but also biodegradable. Here we report that the sensitivity and selectivity of protein nanowire-based sensors can be modified with a simple plug and play genetic approach in which a short peptide sequence, designed to bind the analyte of interest, is incorporated into the pilin protein that is microbially assembled into nanowires. We employed a scalable Escherichia coli chassis to fabricate protein nanowires that displayed either a peptide previously demonstrated to effectively bind ammonia, or a peptide known to bind acetic acid. Sensors comprised of thin films of the nanowires amended with the ammonia-specific peptide had a ca. 100-fold greater response to ammonia than sensors made with unmodified protein nanowires. Protein nanowires with the peptide that binds acetic acid yielded a 4-fold higher response than nanowires without the peptide. The results demonstrate that protein nanowires with enhanced sensor response for analytes of interest can be fabricated with a flexible genetic strategy that sustainably eliminates the energy, environmental, and health concerns associated with other common nanomaterials.

bioengineering↗

bioRxiv2021

Generating Electricity from Water Evaporation Through Microbial Biofilms

Sustainable strategies for energy production are required to reduce reliance on fossil fuels and to power electronics without generating toxic waste.1-7 Generating electricity from water evaporation through engineered materials is a promising approach,8,9 but power outputs have been low and the materials employed were not sustainably produced. Microorganisms can be mass produced with renewable feedstocks. Here, we demonstrate that it is possible to engineer microbial biofilms as a cohesive, flexible material for long-term continuous electricity production from evaporating water. The biofilm sheets were the functional component in devices that continuously produced power densities ([~]1 W/cm2) higher than that achieved with non-biological materials. Current production scaled directly with biofilm-sheet size and skin-patch devices harvested sufficient electricity from the moisture on skin to continuously power wearable devices. The results demonstrate that appropriately engineered biofilms can perform as robust functional materials without the need for further processing or maintaining cell viability. Biofilm-based hydroelectric current production was comparable to that achieved with similar sized biofilms catalyzing current production in microbial fuel cells,10,11 without the need for an organic feedstock or maintaining cell viability. The ubiquity of biofilms in nature suggests the possibility of additional sources of biomaterial for evaporation-based electricity generation and the possibility of harvesting electricity from diverse aqueous environments.

microbiology↗

bioRxiv2021

Pili Expression in Geobacter sulfurreducens Lacking the Putative Gene for the PilB Pilus Assembly Motor

Multiple lines of evidence suggest that electrically conductive pili (e-pili) are an important conduit for long-range electron transport in Geobacter sulfurreducens, a common model microbe for the study of extracellular electron transport mechanisms. One strategy to study the function of e-pili has been to delete the gene for PilB, the pilus assembly motor protein, in order to prevent e-pili expression. However, we found that e-pili are still expressed after the gene for PilB is deleted. Conducting probe atomic force microscopy revealed filaments with the same diameter and similar current-voltage response as e-pili harvested from wild-type G. sulfurreducens or when e-pili are heterologously expressed from the G. sulfurreducens pilin gene in E. coli. Immunogold labeling demonstrated that a G. sulfurreducens strain expressing e-pili with a His-tag continued to express His-tag labelled e-pili when the PilB gene was deleted. Strains with the PilB gene deleted produced maximum current densities comparable to wild-type controls. These results demonstrate that deleting the gene for PilB is not an appropriate strategy for constructing strains of G. sulfurreducens without e-pili, necessitating a reinterpretation of the results of previous studies that have employed this approach. ImportanceGeobacter sulfurreducens is a model microbe for the study of biogeochemically and technologically significant processes such as the reduction of Fe(III) oxides in soils and sediments; bioelectrochemical applications that produce electric current from waste organic matter or drive useful processes with the consumption of renewable electricity; direct interspecies electron transfer in anaerobic digestors and methanogenic soils and sediments; and metal corrosion. The phenotypes associated with gene deletions are an important strategy for determining the mechanisms for extracellular electron transfer in G. sulfurreducens. The results reported here demonstrate that a gene deletion previously thought to prevent the expression of electrically conductive pili in G. sulfurreducens does not have the intended result. Conductive pili continue to be expressed. This finding is important for interpreting the results of several previous studies on conductive pili function.

microbiology↗

bioRxiv2021

Mechanisms for Electron Uptake by Methanosarcina acetivorans During Direct Interspecies Electron Transfer

Direct interspecies electron transfer (DIET) between bacteria and methanogenic archaea appears to be an important syntrophy in both natural and engineered methanogenic environments. However, the electrical connections on the outer surface of methanogens and the subsequent processing of electrons for carbon dioxide reduction to methane are poorly understood. Here we report that the genetically tractable methanogen Methanosarcina acetivorans can grow via DIET in co-culture with Geobacter metallireducens serving as the electron-donating partner. Comparison of gene expression patterns in M. acetivorans grown in co-culture versus pure culture growth on acetate revealed that transcripts for the outer-surface, multi-heme, c-type cytochrome MmcA were higher during DIET-based growth. Deletion of mmcA inhibited DIET. The high aromatic amino acid content of M. acetivorans archaellins suggests that they might assemble into electrically conductive archaella. A mutant that could not express archaella was deficient in DIET. However, this mutant grew in DIET-based co-culture as well as the archaella-expressing parental strain in the presence of granular activated carbon, which was previously shown to serve as a substitute for electrically conductive pili as a conduit for long-range interspecies electron transfer in other DIET-based co-cultures. Transcriptomic data suggesting that the membrane-bound Rnf, Fpo, and HdrED complexes also play a role in DIET were incorporated into a charge-balanced model illustrating how electrons entering the cell through MmcA can yield energy to support growth from carbon dioxide reduction. The results are the first genetics-based functional demonstration of likely outer-surface electrical contacts for DIET in a methanogen. ImportanceThe conversion of organic matter to methane plays an important role in the global carbon cycle and is an effective strategy for converting wastes to a useful biofuel. The reduction of carbon dioxide to methane accounts for approximately a third of the methane produced in anaerobic soils and sediments as well as waste digesters. Potential electron donors for carbon dioxide reduction are H2 or electrons derived from direct interspecies electron transfer (DIET) between bacteria and methanogens. Elucidating the relative importance of these electron donors has been difficult due to a lack of information on the electrical connects on the outer surface of methanogens and how they process the electrons received from DIET. Transcriptomic patterns and gene deletion phenotypes reported here provide insight into how a group of Methanosarcina that play an important role in methane production in soils and sediments participate in DIET.

microbiology↗

bioRxiv2020

Brain state-dependent cortico-hippocampal network dynamics are modulated by postnatal stimuli

Neurons in the cerebral cortex and hippocampus discharge synchronously in a brain state-dependent manner to transfer information. Published studies have highlighted the temporal coordination of neuronal activities between the hippocampus and a cortical area, however, how the spatial extent of cortex activity relates to hippocampal activity remains largely unknown. We imaged macroscopic cortical activity while recording hippocampal local field potentials in unanesthetized GCaMP-expressing transgenic mice. We found that cortical activity elevates before and after hippocampal sharp wave ripples (SWR). SWR-associated cortical activities occurred predominantly in vision-related regions including visual, retrosplenial and prefrontal cortex. While pre-SWR cortical activities were frequently observed in awake and sleep states, post-SWR cortical activity decreased significantly in sleep. During hippocampal theta oscillation states, phase-locked oscillations of calcium activity was observed throughout the entire cortex state. Environmental effects on cortico-hippocampal dynamics were also assessed by comparing mice reared in an enriched environment (ENR) or under isolated conditions (ISO). In both SWR and theta oscillations, mice reared in an isolated condition exhibited clearer brain state-dependent dynamics than those reared in an enriched environment. Our data demonstrate that the cortex and hippocampus exhibit heterogeneous activity patterns that characterize brain states, and postnatal experience plays a significant role in modulating these patterns. Significant StatementThe hippocampus is a center for memory formation. However, the memory formed in the hippocampus is not stored forever, but gradually transferred into the cerebral cortex. As an underlying mechanism, phase-locked synchronized activities between the cortex and hippocampus has been hypothesized. However, spatio-temporal dynamics between hippocampus and whole cortical areas remained mostly unknown. We measured cortical calcium activities with hippocampal electroencephalogram (EEG) simultaneously, and found that the activities of widespread cortical areas are temporally associated with hippocampal EEG. The cortico-hippocampal dynamics is primarily regulated by animal awake/sleep state. Even if similar EEG patters were observed, temporal dynamics between the cortex and hippocampus exhibit distinct patterns between awake and sleep period. In addition, animals postnatal experience modulates the dynamics.

neuroscience↗

bioRxiv2019

An Escherichia coli Chassis for Production of Electrically Conductive Protein Nanowires

Geobacter sulfurreducens pilin-based electrically conductive protein nanowires (e-PNs) are a revolutionary electronic material. They offer novel options for electronic sensing applications and have the remarkable ability to harvest electrical energy from atmospheric humidity. However, technical constraints limit mass cultivation and genetic manipulation of G. sulfurreducens. Therefore, we designed a strain of Escherichia coli to express e-PNs by introducing a plasmid that contained an inducible operon with E. coli genes for type IV pili biogenesis machinery and a synthetic gene designed to yield a peptide monomer that could be assembled into e-PNs. The e-PNs expressed in E. coli, and harvested with a simple filtration method, had the same diameter (3 nm) and conductance as e-PNs expressed in G. sulfurreducens. These results, coupled with the robustness of E. coli for mass cultivation and the extensive E. coli toolbox for genetic manipulation, greatly expands opportunities for large-scale fabrication of novel e-PNs.

synthetic biology↗

bioRxiv2019

Decorating Microbially Produced Protein Nanowires with Peptide Ligands

The potential applications of electrically conductive protein nanowires (e-PNs) harvested from Geobacter sulfurreducens might be greatly expanded if the outer surface of the wires could be modified to confer novel sensing capabilities or to enhance binding to other materials. We developed a simple strategy for functionalizing e-PNs with surface-exposed peptide ligands. The G. sulfurreducens gene for the monomer that assembles into e-PNs was modified to add known peptide ligands at the carboxyl terminus of the monomer. Strains of G. sulfurreducens were constructed that fabricated synthetic e-PNs with a six-histidine His-tag or both the His-tag and a nine-peptide HA-tag exposed on the outer surface. Addition of the peptide ligands did not diminish e-PN conductivity. The abundance of HA-tag in e-PNs was controlled by placing expression of the gene for the synthetic monomer with the HA-tag under transcriptional regulation. These studies suggest broad possibilities for tailoring e-PN properties for diverse applications.

synthetic biology↗

bioRxiv2019

A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans to Conserve Energy to Support Growth from Extracellular Electron Transfer

Conservation of energy to support growth solely from extracellular electron transfer was demonstrated for the first time in a methanogen. Methanosarcina acetivorans grew with methanol as the sole electron donor and the extracellular electron acceptor anthraquione-2,6-disulfonate (AQDS) as the sole electron acceptor when methane production was inhibited with bromoethanesulfonate. Transcriptomics revealed that transcripts for the gene for the transmembrane, multi-heme, c-type cytochrome MmcA were 4-fold higher in AQDS-respiring cells versus methanogenic cells. A strain in which the gene for MmcA was deleted failed to grow via AQDS reduction whereas strains in which other cytochrome genes were deleted grew as well as the wild-type strain. The MmcA-deficient strain grew with the conversion of methanol or acetate to methane, suggesting that MmcA has a specialized role as a conduit for extracellular electron transfer. Enhanced expression of genes for methanol conversion to methyl-coenzyme M and components of the Rnf complex suggested that methanol is oxidized to carbon dioxide in AQDS-respiring cells through a pathway that is similar to methyl-coenezyme M oxidation in methanogenic cells. However, during AQDS respiration the Rnf complex and reduced methanophenazine probably transfer electrons to MmcA, which functions as the terminal reductase for AQDS reduction. Extracellular electron transfer may enable survival of methanogens in dynamic environments in which oxidized humic substances and Fe(III) oxides are intermittently available. The availability of tools for genetic manipulation of M. acetivorans makes it an excellent model microbe for evaluating c-type cytochrome-dependent extracellular electron transfer in Archaea.\n\nImportanceExtracellular electron exchange in Methanosarcina species and closely related Archaea plays an important role in the global carbon cycle and can enhance the speed and stability of anaerobic digestion, an important bioenergy strategy. The potential importance of c-type cytochromes for extracellular electron transfer to syntrophic bacterial partners and/or Fe(III) minerals in some Archaea has been suspected for some time, but the studies with Methanosarcina acetivorans reported here provide the first genetic evidence supporting this hypothesis. The results suggest parallels with Gram-negative bacteria, such as Shewanella and Geobacter species, in which outer-surface c-type cytochromes are an essential component for electrical communication with the extracellular environment. M. acetivorans offers an unprecedented opportunity to study mechanisms for energy conservation from the anaerobic oxidation of one-carbon organic compounds coupled to extracellular electron transfer in Archaea with implications not only for methanogens, but possibly also for anaerobic methane oxidation.

microbiology↗

bioRxiv2018

Syntrophus Conductive Pili Demonstrate that Common Hydrogen-Donating Syntrophs can have a Direct Electron Transfer Option

Syntrophic interspecies electron exchange is essential for the stable functioning of diverse anaerobic microbial communities. Hydrogen/formate interspecies electron transfer (HFIT), in which H2 and/or formate function as diffusible electron carriers, has been considered to be the primary mechanism for electron sharing because most common syntrophs were thought to lack biochemical components, such as electrically conductive pili (e-pili), necessary for direct interspecies electron transfer (DIET). Here we report that Syntrophus aciditrophicus, one of the most intensively studied microbial models for HFIT, produces e-pili and can grow via DIET. Pilin genes likely to yield e-pili were found in other genera of hydrogen/formate-producing syntrophs. The finding that DIET is a likely option for diverse syntrophs that are abundant in many anaerobic environments necessitates a reexamination of the paradigm that HFIT is the predominant mechanism for syntrophic electron exchange within anaerobic microbial communities of biogeochemical and practical significance.

microbiology↗