Transport Cycle Research Articles

Function‐Valued Marked Spatial Point Processes on Linear Networks: Application to Urban Cycling Profiles

ABSTRACTIn the literature on spatial point processes, there is an emerging challenge in studying marked point processes with points being labelled by functions. In this paper, we focus on point processes living on linear networks and, from distinct points of view, propose several mark summary characteristics that are of great use in studying the average association and dispersion of the function‐valued marks. Through a simulation study, we evaluate the performance of our proposed mark summary characteristics, both when marks are independent and when some sort of spatial dependence is evident among them. Finally, we employ our proposed mark summary characteristics to study the spatial structure of urban cycling profiles in Vancouver, Canada.

City mobility patterns during the COVID-19 pandemic: analysis of a global natural experiment.

During the COVID-19 pandemic, changes were seen in city mobility patterns around the world, including in active transportation (walking, cycling, micromobility, and public transit use), creating a unique opportunity for global public health lessons and action. We aimed to analyse a global natural experiment exploring city mobility patterns during the pandemic and how they related to the implementation of COVID-19-related policies. We obtained data from Apple's Mobility Trends Reports on city mobility indexes for 296 cities from Jan 13, 2020 to Feb 4, 2022. Mobility indexes represented the frequency of Apple Maps queries for driving, walking, and public transit journeys relative to a baseline value of 100 for the pre-pandemic period (defined as Jan 13, 2020). City mobility index trajectories were plotted with stratification by country income level, transportation-related city type, population density, and COVID-19 pandemic severity (SARS-CoV-2 infection rate). We also synthesised global pandemic policies and recovery actions that promoted or restricted city mobility and active transportation (walking, cycling and micromobility, and public transit) using the Shifting Streets dataset. Additionally, a natural experiment on a global scale evaluated the effects of new active transportation policies on walking and public transit use in cities around the world. We used multivariable regression with a difference-in-difference (DID) analysis to explore whether the implementation of walking or public transit promotion policies affected mobility indexes, comparing cities with and without implementation of these policies in the pre-intervention period (Jan 27 to April 12, 2020) and post-intervention period (April 13 to June 28, 2020). Based on city mobility index trajectories, we observed an overall decline in mobility indexes for walking, driving, and public transit at the beginning of the pandemic, but these values began to increase in April, 2020. Cities with lower population densities generally had higher driving and walking indexes than cities with higher population density, while cities with higher population densities had higher public transit indexes. Cities with higher pandemic severity generally had higher driving and walking indexes than cities with lower pandemic severity, while cities with lower pandemic severity had higher public transit indexes than other cities. We identified 587 policies in the dataset that had known implementation dates and were relevant to active transportation, which included 305 policies on walking, 321 on cycling and micromobility, and 143 on public transit, across 230 cities within 33 countries (19 high-income, 11 middle-income, and three low-income countries). In the global natural experiment (including 39 cities), implementation of policy interventions promoting walking was significantly associated with a higher absolute value of the walking index (DID coefficient 20·675 [95% CI 8·778-32·572]), whereas no such effect was seen for public transit-promoting policies (0·600 [-13·293 to 14·494]). Our results suggest that the policies implemented to mitigate the COVID-19 pandemic were effective in changing city mobility patterns, especially increasing active transportation. Given the known benefits of active transportation, such policies could be maintained, expanded, and evaluated post pandemic. The discrepancy in the interventions between countries of different incomes highlights that changes to the infrastructure to prioritise safe walking, cycling, and easy access to public transit use could help with the future-proofing of cities in low-income and middle-income countries. None.

AI-driven mechanistic analysis of conformational dynamics in CNNM/CorC Mg2+ transporters.

The CNNM/CorC Mg2+ transporters are widely conserved in eukaryotes (cyclin M [CNNM]) and prokaryotes (CorC) and participate in various biological processes. Previous structural analyses of the CorC transmembrane domain in the Mg2+-bound inward-facing conformation revealed the conserved Mg2+ recognition mechanism in the CNNM/CorC family; however, the conformational dynamics in the Mg2+ transport cycle remain unclear because structures in other conformations are unknown. Here, we used AlphaFold structure prediction to predict the occluded-like and outward-facing-like conformations of the CorC and CNNM proteins and identified conserved hydrophilic interactions close to the cytoplasmic side in these conformations. Molecular dynamics simulations and biochemical cross-linking showed that these conserved hydrophilic interactions are stable, especially in the outward-facing-like conformation. Furthermore, mutational analysis revealed that the residues involved in these hydrophilic interactions on the cytoplasmic side are important for Mg2+ transport in the CorC and CNNM proteins. Our work provides mechanistic insights into the transport cycle of the CNNM/CorC family.

Impact of Senescent Cell-Derived Extracellular Vesicles on Innate Immune Cell Function.

Extracellular vesicles (EVs) are components of the senescence-associated secretory phenotype (SASP) that influence cellular functions via their cargo. Here, the interaction between EVs derived from senescent (SEVs) and non-senescent (N-SEVs) fibroblasts and the immune system is investigated. Via endocytosis, SEVs are phagocytosed by monocytes, neutrophils, and B cells. Studies with the monocytic THP-1 cell line find that pretreatment with SEVs results in a 32% (p < 0.0001) and 66% (p < 0.0001) increase in lipopolysaccharide (LPS)-induced tumor necrosis factor-alpha (TNF-α) production when compared to vehicle control or N-SEVs respectively. Interestingly, relative to vehicle control, THP-1 cells exposed to N-SEVs exhibit a 20% decrease in TNF-α secretion (p < 0.05). RNA sequencing reveals significant differences in gene expression in THP-1 cells treated with SEVs or N-SEVs, with vesicle-mediated transport and cell cycle regulation pathways featuring predominantly with N-SEV treatment, while pathways relating to SLITS/ROBO signaling, cell metabolism, and cell cycle regulation are enriched in THP-1 cells treated with SEVs. Proteomic analysis also reveals significant differences between SEV and N-SEV cargo. These results demonstrate that phagocytes and B cells uptake SEVs and drive monocytes toward a more proinflammatory phenotype upon LPS stimulation. SEVs may therefore contribute to the more proinflammatory immune response seen with aging.

Control of dissolved H2 concentration enhances electron generation, transport and TCE reduction by indigenous microbial community

Electrokinetic enhanced bioremediation (EK-Bio) is practical for trichloroethene (TCE) dechlorination because the cathode can produce a wide range of dissolved H2 (DH) concentrations of 1.3–0 mg/L from the electrode to the aquifer. In this study, TCE dechlorination was investigated under different DH concentrations. The mechanisms were discussed by analyzing the microbial community structure and abundance of organohalide-respiring bacteria (OHRB) using 16S rRNA, and the gene abundances of key enzymes in the TCE electron transport chain using metagenomic analysis. The results showed that the moderate DH concentration of 0.19–0.53 mg/L exhibited the most pronounced TCE dechlorination, even better than the higher DH concentrations, due to the optimal redox environment, the enrichments of OHRB, reductive dehalogenase (rdhA) genes and key enzyme genes in the electron generation and transport chain. More electrons were obtained from H2 metabolism by Dehalobacter by promoting the formation of [NiFe] hydrogenase (HupS/L/C) or from glycolysis by versatile OHRB by stimulating the formation of formate and enriching formate dehydrogenase (FDH) under moderate DH conditions. In addition, the enhanced amino acid metabolism improved the vitamin K cycle for electron transport and enriched the reductive dechlorinating enzyme (RDase) genes. This study identifies the optimal DH concentration that facilitates bioremediation efficiency, provides insights into microbial community shifts and key enzymatic pathways in EK-Bio remediation.

Estimating Vertical Distribution of Total Suspended Matter in Coastal Waters Using Remote-Sensing Approaches

The vertical distribution of the marine total suspended matter (TSM) concentration significantly influences marine material transport, sedimentation processes, and biogeochemical cycles. Traditional field observations are constrained by limited spatial and temporal coverage, necessitating the use of remote-sensing technology to comprehensively understand TSM variations over extensive areas and periods. This study proposes a remote-sensing approach to estimate the vertical distribution of TSM concentrations using MODIS satellite data, with the Bohai Sea and Yellow Sea (BSYS) as a case study. Extensive field measurements across various hydrological conditions and seasons enabled accurate reconstruction of in situ TSM vertical distributions from bio-optical parameters, including the attenuation coefficient, particle backscattering coefficient, particle size, and number concentration, achieving a determination coefficient of 0.90 and a mean absolute percentage error of 26.5%. In situ measurements revealed two distinct TSM vertical profile types (vertically uniform and increasing) and significant variation in TSM profiles in the BSYS. Using surface TSM concentrations, wind speed, and water depth, we developed and validated a remote-sensing approach to classify TSM vertical profile types, achieving an accuracy of 84.3%. Combining this classification with a layer-to-layer regression model, we successfully estimated TSM vertical profiles from MODIS observation. Long-term MODIS product analysis revealed significant spatiotemporal variations in TSM vertical distributions and column-integrated TSM concentrations, particularly in nearshore regions. These findings provide valuable insights for studying marine sedimentation and biological processes and offer a reference for the remote-sensing estimation of the TSM vertical distribution in other marine regions.

Structural basis of thiamine transport and drug recognition by SLC19A3

Thiamine (vitamin B1) functions as an essential coenzyme in cells. Humans and other mammals cannot synthesise this vitamin de novo and thus have to take it up from their diet. Eventually, every cell needs to import thiamine across its plasma membrane, which is mainly mediated by the two specific thiamine transporters SLC19A2 and SLC19A3. Loss of function mutations in either of these transporters lead to detrimental, life-threatening metabolic disorders. SLC19A3 is furthermore a major site of drug interactions. Many medications, including antidepressants, antibiotics and chemotherapeutics are known to inhibit this transporter, with potentially fatal consequences for patients. Despite a thorough functional characterisation over the past two decades, the structural basis of its transport mechanism and drug interactions has remained elusive. Here, we report seven cryo-electron microscopy (cryo-EM) structures of the human thiamine transporter SLC19A3 in complex with various ligands. Conformation-specific nanobodies enable us to capture different states of SLC19A3’s transport cycle, revealing the molecular details of thiamine recognition and transport. We identify seven previously unknown drug interactions of SLC19A3 and present structures of the transporter in complex with the inhibitors fedratinib, amprolium and hydroxychloroquine. These data allow us to develop an understanding of the transport mechanism and ligand recognition of SLC19A3.

EDDS application destabilizes soil organic matter in phytoremediation: Insights from quantity and molecular composition of dissolved organic matter

The stability of soil organic matter (SOM) is crucial for metal transport and carbon cycling. S,S-ethylenediaminedisuccinic acid (EDDS) is widely used to enhance phytoremediation efficiency for heavy metals in contaminated soils, yet its specific impacts on SOM have been underexplored. This study investigates the effects of EDDS on SOM stability using a rhizobox experiment with ryegrass. Changes in soil dissolved organic matter (DOM) quantity and molecular composition were analyzed via Fourier transform ion cyclotron resonance mass spectrometry. Results showed that the use of EDDS increased the uptake of Cu, Cd and Pb by ryegrass, but simultaneously induced the destabilization and transformation of SOM. After 7 days of EDDS application, dissolved organic carbon (DOC) and nitrogen (DON) concentrations in rhizosphere soils increased significantly by 3.44 and 10.2 times, respectively. In addition, EDDS reduced lipids (56.3%) and proteins/amino sugars-like compounds (52.1%), while increasing tannins (9.11%) and condensed aromatics-like compounds (24.4%) in the rhizosphere DOM. These effects likely stem from EDDS's dual action: extracting Fe/Al from SOM-mineral aggregates, releasing SOM into the DOM pool, and promoting microbial degradation of bioavailable carbon through chain scission and dehydration. Our study firstly revealed that the application of EDDS in phytoremediation increased the mineralization of SOM and release of CO2 from soil to the atmosphere, which is important to assess the carbon budget of phytoremediation and develop climate-smart strategy in future.

Exploring global oceanic persistence and ecological effects of legacy persistent organic pollutants across five decades.

Global monitoring of persistent organic pollutants (POPs) has intensified following regulatory efforts aimed at reducing their release. In this context, we compiled over 10,000 POP measurements, reported from 1980 to 2023, to assess the effectiveness of these legislative measures in the global marine environments. While a general decreasing trend in legacy POP concentrations is evident across various maritime regions, highlighting the success of source control measures, the Arctic Ocean and its marginal seas have experienced a rise in POP levels. This increase suggests the northward migration of pollutants via ocean currents from mid-latitude regions to polar areas. Despite global efforts to reduce emissions, the continued transport and accumulation of pollutants to the Arctic regions may have substantial ecological impacts. Addressing these environmental challenges demands a thorough understanding of POP dynamics, including response times, multiphase transport, and biogeochemical cycling. Continued research into these processes is vital to accurately map their distribution and temporal variations within marine systems.

Computationally accelerated identification of P-glycoprotein inhibitors.

Overexpression of the polyspecific efflux transporter, P-glycoprotein (P-gp, MDR1, ABCB1 ), is a major mechanism by which cancer cells acquire multidrug resistance (MDR), the resistance to diverse chemotherapeutic drugs. Inhibiting drug transport by P-gp can resensitize cancer cells to chemotherapy, but there are no P-gp inhibitors available to patients. Clinically unsuccessful P-gp inhibitors tend to bind at the pump's transmembrane drug binding domains and are often P-gp transport substrates, resulting in lowered intracellular concentration of the drug and altered pharmacokinetics. In prior work, we used computationally accelerated drug discovery to identify novel P-gp inhibitors that target the pump's cytoplasmic nucleotide binding domains. Our first-draft study provided conclusive evidence that the nucleotide binding domains of P-gp are viable targets for drug discovery. Here we develop an enhanced, computationally accelerated drug discovery pipeline that expands upon our prior work by iteratively screening compounds against multiple conformations of P-gp with molecular docking. Targeted molecular dynamics simulations with our homology model of human P-gp were used to generate docking receptors in conformations mimicking a putative drug transport cycle. We offset the increased computational complexity using custom Tanimoto chemical datasets, which maximize the chemical diversity of ligands screened by docking. Using our expanded, virtual-assisted pipeline, we identified nine novel P-gp inhibitors that reverse MDR in two types of P-gp overexpressing human cancer cell lines, reflecting a 13.4% hit rate. Of these inhibitors, all were non-toxic to non-cancerous human cells, and six were not likely to be transport substrates of P-gp. Our novel P-gp inhibitors are chemically diverse and are good candidates for lead optimization. Our results demonstrate that the nucleotide binding domains of P-gp are an underappreciated target in the effort to reverse P-gp-mediated multidrug resistance in cancer.

Structural Models of Human Norepinephrine Transporter Ensemble Reveal the Allosteric Sites and Ligand-Binding Mechanism.

The norepinephrine transporter (NET) plays a pivotal role in recycling norepinephrine (NE) from the synaptic cleft. However, the structures referring to the conformational heterogeneity of NET during the transport cycle remain poorly understood. Here, three structural models of NE bound to the orthosteric site of NET in outward-open (OOholo), outward-occluded (OCholo), and inward-open (IOholo) conformations were first obtained using the multistate structures of serotonin transporter as templates and further characterized through Gaussian-accelerated molecular dynamics and free energy reweighting. Analysis of the structures revealed eight potential allosteric sites on the functional-specific states of NET. One of the pharmacologically relevant pockets located at the extracellular vestibule was further verified by simulating the binding behaviors of a clinical trial drug χ-MrIA that is allosterically regulating NET. These structural and energetic insights into NET advanced our understanding of NE reuptake and paved the way for discovering novel molecules targeting the allosteric sites.

Computer vision and statistical insights into cycling near miss dynamics

Across the globe, many transport bodies are advocating for increased cycling due to its health and environmental benefits. Yet, the real and perceived dangers of urban cycling remain obstacles. While serious injuries and fatalities in cycling are infrequent, “near misses”-events where a person on a bike is forced to avoid a potential crash or is unsettled by a close vehicle-are more prevalent. To understand these occurrences, researchers have turned to naturalistic studies, attaching various sensors like video cameras to bikes or cyclists. This sensor data holds the potential to unravel the risks cyclists face. Still, the sheer amount of video data often demands manual processing, limiting the scope of such studies. In this paper, we unveil a cutting-edge computer vision framework tailored for automated near-miss video analysis and for detecting various associated risk factors. Additionally, the framework can understand the statistical significance of various risk factors, providing a comprehensive understanding of the issues faced by cyclists. We shed light on the pronounced effects of factors like glare, vehicle and pedestrian presence, examining their roles in near misses through Granger causality with varied time lags. This framework enables the automated detection of multiple factors and understanding their significant weight, thus enhancing the efficiency and scope of naturalistic cycling studies. As future work, this research opens the possibility of integrating this AI framework into edge sensors through embedded AI, enabling real-time analysis.

Transport mechanism and structural pharmacology of human urate transporter URAT1

Urate is an endogenous product of purine metabolism in the liver. High urate levels in the blood lead to gout, a very common and painful inflammatory arthritis. Excreted urate is reabsorbed in the kidney mainly by URAT1 antiporter, a key target for anti-gout drugs. To uncover the mechanisms of urate transport and drug inhibition, we determined cryo-EM structures of human URAT1 with urate, counter anion pyrazinoate, or anti-gout drugs of different chemotypes — lesinurad, verinurad, and dotinurad. We captured the outward-to-inward transition of URAT1 during urate uptake, revealing that urate binds in a phenylalanine-rich pocket and engages with key gating residues to drive the transport cycle. In contrast to the single binding site for urate, pyrazinoate interacts with three distinct, functionally relevant sites within URAT1, a mechanism that has not yet been observed in other anion antiporters. In addition, we found that while all three drugs compete with substrates and halt the transport cycle, verinurad and dotinurad further hijack gating residues to achieve high potency. These insights advance our understanding of organic anion transport and provide a foundation for designing improved gout therapeutics.

The effects of built environments on bicycle accidents around bike-sharing program stations using street view images and deep learning techniques: The moderating role of streetscape features

With the global rise of bike-sharing programs (BSP), planners and traffic experts have raised concerns as to whether the rapid growth of BSP ensures cycling safety. Despite numerous studies on built environments encouraging bike usage, there is limited knowledge whether streetscape environments around BSP stations affect bicycle accidents. We address this gap by investigating the relationships between various built environments and bicycle accidents around BSP stations, with a particular focus on the moderating effects of comprehensive streetscapes. Streetscape environments, estimated through semantic segmentation and k-means clustering, were used in two-level negative binomial regression models to clarify how street- and station-level environments affect different types of bicycle accidents. The findings indicate increased crash likelihoods on higher-speed roads, streets with traffic facilities, in proximity to public transportation infrastructure, and specific streetscape types. In particular, streetscape features like green oasis streets and open-sky roadways positively contribute to mitigating the negative effects of traffic facilities, such as bike networks and crosswalks, on cycling safety. This study aids in developing comprehensive strategies and guidelines to retrofit built environments for better traffic safety and thereby promote urban cycling.

Structural insights into human ABCD3-mediated peroxisomal acyl-CoA translocation

Human ABC transporters ABCD1–3 are all localized on the peroxisomal membrane and participate in the β-oxidation of fatty acyl-CoAs, but they differ from each other in substrate specificity. The transport of branched-chain fatty acids from cytosol to peroxisome is specifically driven by ABCD3, dysfunction of which causes severe liver diseases such as hepatosplenomegaly. Here we report two cryogenic electron microscopy (cryo-EM) structures of ABCD3 bound to phytanoyl-CoA and ATP at resolutions of 2.9 Å and 3.2 Å, respectively. A pair of phytanoyl-CoA molecules were observed in ABCD3, each binding to one transmembrane domain (TMD), which is distinct from our previously reported structure of ABCD1, where each fatty acyl-CoA molecule strongly crosslinks two TMDs. Upon ATP binding, ABCD3 exhibits a conformation that is open towards the peroxisomal matrix, leaving two extra densities corresponding to two CoA molecules deeply embedded in the translocation cavity. Structural analysis combined with substrate-stimulated ATPase activity assays indicated that the present structures might represent two states of ABCD3 in the transport cycle. These findings advance our understanding of fatty acid oxidation and the molecular pathology of related diseases.

51 She Moves - A comparative study examining the perception of the built environment between men and women

Abstract Sustainable urban transport and active travel are part of policy and practice worldwide, with a strong focus on strengthening the relationship between transport and health (US PHA, 2021; NICE, 2012; EU Commission, 2013; ISPAH, 2020). The gap we see in physical activity with males globally being more active than their female counterparts is also evident in transport, with a male bias in planning and design and gender a determinant in modal choice (UN, 2017; ITF, 2018; TII, 2019). This research aims to explore the perceptions of the built environment from a male and female perspective and how this implicates physical activity levels. Walking and cycling for active transport have substantial health benefits, however women are less inclined to use AT than men (Mueller et al, 2015; Garrad et al, 2008; Heesch &amp; Sahlqvist, 2013). This is due to the gendered nature of cites being designed for the use of men and not women (Bassam, 2023). This study utilised a quantitative approach. A survey was made available nationally (Ireland) on Microsoft Forms, it was available to all genders and both rural and urban individuals. The aim of this survey is gather an in depth understanding of women’s perceptions of the built environment and it’s correlation to activity levels, active travel behaviour and health, and how this differs to men. The Healthy Ireland protocol has been used to gather baseline data, general health and demographic information. The findings have been analysed using SPSS. The results of this study will be complete before August 2024. The survey is currently available to be completed online. Results are to be published in an academic journal. The aim of this study is to highlight the difference in perceptions of an individuals built environment dependent on gender. The results from this study will inform policy surrounding the design of cities and towns with infrastructure that is accessible and u​tilized by all. It will inform how we redesign cities for the use of all and have a gender-neutral perspective on city design, active travel and transport. Support/Funding Source This research has been funded by Technological University Dublin.

Transport of herbicides by PIN-FORMED auxin transporters.

Auxins are a group of phytohormones that control plant growth and development 1. Their crucial role in plant physiology has inspired development of potent synthetic auxins that can be used as herbicides 2. Phenoxyacetic acid derivatives are a widely used group of auxin herbicides in agriculture and research. Despite their prevalence, the identity of the transporters required for distribution of these herbicides in plants is both poorly understood and the subject of controversial debate 3,4. Here we show that PIN-FORMED auxin transporters transport a range of phenoxyacetic acid herbicides across the membrane and we characterize the molecular determinants of this process using a variety of different substrates as well as protein mutagenesis to control substrate specificity. Finally, we present Cryo-EM structures of Arabidopsis thaliana PIN8 with 2,4-dichlorophenoxyacetic acid (2,4-D) or 4-chlorophenoxyacetic acid (4-CPA) bound. These structures represent five key states from the transport cycle, allowing us to describe conformational changes associated with substrate binding and transport across the membrane. Overall, our results reveal that phenoxyacetic acid herbicides use the same export machinery as endogenous auxins and exemplify how transporter binding sites undergo transformations that dictate substrate specificity. These results enable development of novel synthetic auxins and for guiding precision breeding of herbicide resistant crop plants.

Which street characteristics support cycling for transport among vulnerable groups in traffic: A think-aloud study in virtual reality

Although several health benefits are associated with cycling, this mode of active transport remains underrepresented. Studies have shown that individuals' preferred mode of transport is influenced by the environment in which they travel. While macro-environmental factors shape active transport, micro-environmental aspects offer adaptable solutions. In this paper, we used novel and promising Virtual Reality (VR) technology to investigate which street characteristics regarding safety and attractiveness are important for promoting cycling for transport in three vulnerable groups in traffic, i.e., adolescents, adults with a low SES, and older adults. Participants cycled through two virtual streets based on existing streets in Ghent, Belgium. The think-aloud method was used to collect qualitative data during cycling and afterward participants were asked to fill in a questionnaire about the VR experience, self-reported cycling behavior, and sociodemographic factors. Transcribed files were analyzed using content analysis, revealing 14 crucial street characteristics. Separate cycling paths, clear markings and traffic signs, even surfaces, calm streets, spacious layouts, and aesthetically pleasing environments were found to be important by all target groups. Adolescents and older adults emphasized slower traffic, visibility, wider cycle paths, high curbs, and sudden unexpected actions. Secure bicycle parking was crucial for adolescents, while older adults valued green environments and had mixed opinions on traffic-calming structures. This study underscores the significance of micro-scale street features in promoting active transport among vulnerable groups. Additionally, it demonstrates the potential of VR for inclusive urban design and citizen-based science.

Direct detection of the chloride release and uptake reactions of Natronomonas pharaonis halorhodopsin

Membrane transport proteins undergo multistep conformational changes to fulfill the transport of substrates across biological membranes. Substrate release and uptake are the most important events of these multistep reactions that accompany significant conformational changes. Thus, their relevant structural intermediates should be identified to better understand the molecular mechanism. However, their identifications have not been achieved for most transporters due to the difficulty of detecting the intermediates. Herein, we report the success of these identifications for a light-driven chloride transporter halorhodopsin (HR). We compared the time course of two flash-induced signals during a single transport cycle. One is a potential change of Cl--selective membrane, which enabled us to detect tiny Cl--concentration changes due to the Cl- release and the subsequent Cl--uptake reactions by HR. The other is the absorbance change of HR reflecting the sequential formations and decays of structural intermediates. Their comparison revealed not only the intermediates associated with the key reactions but also the presence of two additional Cl--binding sites on the Cl--transport pathways. The subsequent mutation studies identified one of the sites locating the protein surface on the releasing side. Thus, this determination also clarified the Cl--transport pathway from the initial binding site until the release to the medium.

Influence of cascade reservoirs on the distribution, transport, and retention patterns of biogenic elements in the Jinsha River

Cascade reservoirs construction can greatly alter flow regime and sediment transport of rivers, further affecting migration and transformation processes of biogenic elements. The Jinsha River (JSR) is the China's largest hydropower base and the main runoff, sediment suspension, and nutrient source areas of the Yangtze River. However, the distribution, transport, and retention patterns of biogenic elements in the JSR are still unclear under the influence of cascade reservoirs. Therefore, monthly concentration monitoring work was conducted from November 2021 to October 2023 for various forms of carbon (C), nitrogen (N), phosphorus (P), and silicon (Si). Results showed that the concentrations and fluxes of total phosphorus (TP) and particulate phosphorus (PP) exhibited continuous decreasing trends along the reservoirs cascade, whereas N exhibited contrasting trends. The concentrations of dissolved total carbon (DTC), dissolved inorganic carbon (DIC), and total silicon also showed decreasing trends from upstream to downstream, whereas their fluxes were primarily influenced by runoff and exhibited upward fluctuations. Compared with other biogenic elements, there was a more pronounced retention effect on TP and PP by reservoirs, with average retention rates of 8.29 % and 16.01 %, respectively. Longer hydraulic retention time (HRT) can retain more TP and PP. Meanwhile, the retention rates of DTC, DIC, and particulate silicon were positively correlated with HRT, while the retention rate of dissolved silicon (DSi) showed a positive correlation with reservoir age. Moreover, the higher ratios of dissolved inorganic nitrogen to dissolved inorganic phosphorus (DIP) and DSi to DIP have occurred, resulting in apparent P limitation, particularly during the non-flood season due to lower DIP concentration. Overall, cascade reservoirs construction exists great influences on the spatial allocation, fluxes transport, and biogeochemical cycles of biogenic elements, potentially affecting the stability of rivers ecosystem along the food chain network.