Understanding Spatial and Temporal Scale in Biology

How do you measure the mechanical forces generated by single cells? What are the cues that guide cell migration? What are the interactions between cells that account for cooperative behaviors among cells? To answer these and many other basic questions about biological function, we must have the

近年来国内森林生态系统服务功能研究较多,但应用价值不高,其科学性受到诸多质疑。从森林水源涵养功能的多尺度内涵、过程以及其计量方法出发,对国内外研究动态和发展趋势进行了总结分析,重新审视森林水源涵养功能的研究意义,探讨森林水源涵养功能的多尺度特征。从森林水源涵养功能作用的空间尺度上看,其拦蓄洪水削减洪峰的功能仅在较小尺度上有效,而调节径流的功能只有当森林土壤的入渗量超过蒸散量时,才可能有更多地下水补给河道径流,进而增加旱季河道流量。同时森林水源涵养功能也具有明显的时间尺度特征,具体表现为在次降水事件中,由于蒸散发量较小,森林水源涵养功能的物质量等于森林不同层次的截留量,在功能上表现为拦蓄降水;在长时间尺度上,由于林地蒸散要耗去大量水分,森林水源涵养功能的物质量等于森林不同层次的截留量减去林地蒸散发量,在功能上表现为净化水质和调节径流。大多数研究仅对单一林分的个别层次蓄水功能进行研究,缺乏流域尺度或者更大空间尺度的森林水源涵养功能研究。建议从区域降尺度到流域或将坡面尺度上推到流域,集中在流域尺度解决森林水源涵养空间异质性将是解决森林水源涵养功能尺度外推的有效办法。就目前国内流行的森林水源涵养功能计量方法而言,其与尺度及研究目的有较大相关性,在研究中应根据研究目的、研究尺度和可获取的数据情况选择合适的计量方法。研究突出了不同尺度作用下森林水文过程的复杂性及重要性,并结合森林与水关系的争论问题,分析目前国内对森林水源涵养功能研究的一些误区,提出森林水源涵养功能研究的一些关键科学问题及未来可能的发展方向,主要包括:1)明确界定森林水源涵养功能的边界,探索森林水源涵养功能计量的新方法;2)加强不同时空尺度关联的森林水源涵养功能研究,包括正确评价森林水源涵养功能的时空变异规律,森林生态系统水源涵养功能的尺度效应,森林水源涵养与下游水生态安全,森林水源涵养研究范式转变等核心问题。;Forest water conservation as an important ecosystem function has caused a rising interests in the scientific community in recent years. However, there remain some arguments in several aspects regarding the forest water conservation function. For the concept of the forest water conservation, there is no clear definition about its connotation. Another concern is the scaling issue. It is a challenge to scale up the estimation for the forest water conservation from the plot scale to larger scale, e.g., watershed scale or regional scale. Many quantification methods have been developed, but their suitability, performance, advantages and disadvantages are unknown. Many of such argument issues are significant limits of the forest water conservation in science and management. On the basis of the literature review, we clarify the important role of the water conservation in forest ecosystem function. We also summarize and analyze the concepts of the forest water conservation and its multi-scale connotation, processes and quantification methods. On the spatial scale, function of the forest in mitigating peak flow is effective at a smaller scale but not necessarily at a larger scale. More groundwater recharges into stream flow when forest soil infiltration exceeds evapotranspiration, thus increasing stream flow in the dry season. During a rainfall event, forest water conservation has different features at different temporal scales. For example, the amount of the forest conservation during a rainfall event dominates by the forest canopy interception and most water is stored in the forest due to less evapotranspiration in the rainfall event scale. At the longer temporal scale, the forest water conservation can be determined by the forest canopy interception subtracting evapotranspiration. The functional roles of the forest water conservation at longer temporal scale dominate by purifying water from natural rainfall and mitigating seasonal flow peaks of the river discharges. Most previous studies of the forest water conservation focused on water storage function at the plot scale, but lack better understanding in the forest water conservation function at the watershed or regional scales. We suggest the approach that combines downscaling from the regional to watershed scales and upscaling from the hillside to the watershed scales can an effective way of the scale extrapolation. This idea can be used to address the heterogeneity issue of the forest water conservation function at different spatio-temporal scales. Among the existing quantification approaches of the forest water conservation function, each one highly relies on the temporal and spatial scales and its application goal. An appropriate calculation method should be carefully evaluated and considered based on the objectives, data availability, temporal and spatial scales of each study case. The suitability difference in different calculation methods of the forest water conservation demonstrates the complexity and importance of the multi-scale consideration in forest hydrological processes. In the context of the long-term debates about the relationship between the forest and water, we figure out a few confusing points in the current studies of the forest water conservation function. We also propose the critical scientific questions that should be addressed and a few directions in future studies of forest water conservation function including: 1) to clearly define the connotation and boundary of the forest water conservation function, and develop innovatory methods for determining the forest water conservation function; 2) to pay more attentions on the forest water conservation function studies associated with the different spatial and temporal scales, including evaluation of the spatio-temporal variations in forest water conservation function, the scaling effects on estimation of the water conservation function, the trade-off relationship between the upstream forest water conservation and the downstream ecological water need, and the development of the innovatory ways of forest water conservation practices.

This study focused on the structure of the aquatic insect community in spatial and temporal scales in the Esparza River. The river was sampled for one full year throughout 2007. During the dry season low flow months, five sampling points were selected in two different habitats (currents and pools), with five replicates per sample site. During the wet season with peak rain, only the data in the "current habitat" were sampled at each site. Specimens present in the different substrates were collected and preserved in situ. A nested ANOVA was then applied to the data to determine richness and density as the response variables. The variations in temporal and spatial scales were analyzed using width, depth and discharge of the river, and then analyzed using a nested ANOVA. Only a correlation of 51% similarity in richness was found, while in spatial scale, richness showed significant variation between sampling sites, but not between habitats. However, the temporal scale showed significant differences between habitats. Density showed differences between sites and habitats during the dry season in the spatial scale, while in the temporal scale significant variation was found between sampling sites. Width varied between habitats during the dry season, but not between sampling points. Depth showed differences between sampling sites and season. This work studies the importance of community structure of aquatic insects in rivers, and its relevance for the quality of water in rivers and streams.

Leveraging microfluidics and nano-plasmonics, we present in this paper a new method employing a micro-nano-device that is capable of monitoring the dynamic cell-substrate attachment process at single cell level in real time without labeling. The micro-nano-device essentially has a gold thin film as the substrate perforated with periodic, near-cm2-area, template-stripped nano-holes, which generate plasmonic extraordinary optical transmission (EOT) with a high sensitivity to refractive index changes at the metal-dielectric interface. Using this device, we successfully demonstrated label-free and real-time monitoring of the dynamic cell attachment process for single mouse embryonic stem cell (C3H10) and human tumor cell (HeLa) by collecting EOT spectrum data during 3-hour on-chip culture. We further collected the EOT spectral shift data at the start and end points of measurement during 3-hour on-chip culture for 50 C3H10 and 50 HeLa cells, respectively. The experiment results show that the single cell attachment process of both HeLa and C3H10 cells follow the logistic retarded growth model, but with different kinetic parameters. Variations in spectral shift during the same culture period across single cells present new evidence for cell heterogeneity. The micro-nano-device provides a new, label-free, real-time, and sensitive, platform to investigate the cell adhesion kinetics at single cell level.

Healthy ecosystems such as forests and wetlands have a great potential to support adaptation to climate change and are the foundation of sustainable livelihoods. Ecosystem-based adaptation (EbA) can help to protect and maintain healthy ecosystems providing resilience against the impacts of climate change. This paper explores the role of EbA in reconciling socio-economic development with the conservation and restoration of nature in Lake Victoria Basin, Kenya, East Africa. Using selected ecosystems in the Lake region, the paper identifies key EbA approaches and explores trade-offs and synergies at spatial and temporal scales and between different stakeholders. The research methods used for this study include site visits, key informant interviews, focus group discussions, participatory workshops and literature reviews. An analytical framework is applied to advance the understanding of EbA approaches and how they lead to synergies and trade-offs between ecosystem services provision at spatial and temporal scales and multiple stakeholders. Our results show that EbA approaches such as ecosystem restoration have the potential to generate multiple adaptation benefits as well as synergies and trade-offs occurring at different temporal and spatial scales and affecting various stakeholder groups. Our paper underscores the need to identify EbA trade-offs and synergies and to explore the ways in which they are distributed in space and time and between different stakeholders to design better environmental and development programmes.

A whole-lake acoustic telemetry array was utilized to monitor the three-dimensional position of 20 largemouth bass (Micropterus salmoides). Code division multiple access (CDMA) technology enabled the simultaneous monitoring of the 20 transmitters (equipped with pressure and temperature sensors) at 15 s intervals with sub-meter accuracy. Fish were monitored between November 2003 and April 2004 to evaluate the behaviour of fish across different temporal and spatial scales. The distance moved by largemouth bass, assessed both on a daily and hourly basis, varied by season and was positively correlated with water temperature. For example, daily movement rates were 2.69 ± 1.45 km/day in mid November (average daily water temperature 5.9°C), 2.24 ± 0.73 km/day in early January (5.1°C), and 7.28 ± 2.62 km/day in mid April (7.7°C). Interestingly, daily movement rates varied by as much as 25 fold among individual fish. Visualization of fish swimming paths revealed that whereas some fish occupied discrete areas and made only localized movements, other individuals made lengthier journeys covering much of the lake in periods of as little as one day. Analysis of fish behaviour at a finer temporal scale revealed that during the winter, fish spend more than 95% of their time swimming at speeds less than 0.1 m/s (0.07 ± 0.24 m/s). During late fall, and especially in spring, swimming speeds were higher with mean swimming speeds of 0.11 ± 0.27 m/s and 0.19 ± 0.29 m/s, respectively. When the telemetry dataset was queried to simulate 24 h manual tracking intervals, it was clear that manual tracking data would not have been representative of actual daily movement rates, underestimating daily movement and swimming speeds by at least 75 fold. This study identifies the importance of evaluating fish activity at multiple spatial (whole lake to sub-meter position) and temporal (seasonal to seconds) scales and illustrates the potential of CDMA telemetry to yield such data.

Relationships between land use and water quality of rivers and lakes vary spatially and temporally. These variations were analyzed using spatial analysis and mathematical statistical methods for the Suzhou Creek in Shanghai. Based on the data of water quality and land use in 2001， 2005， 2010， 2015， and 2020， five spatial scales （200， 500， 1 000， 2 000， and 5 000 m reach buffer） of the landscape pattern were extracted using correlation and redundancy analysis to explore the impact of land use composition and spatial pattern on water quality at different spatial and temporal scales. The results showed that： ① the water quality of Suzhou Creek has gradually improved in the past 20 years； other indicators were between Class II to Class IV in 2020 except TN， and TN was the main pollutant. ② The main land use type of the buffer zone was construction land， and the proportion of greenland and woodland showed a small growth trend. ③ The water quality was closely related to landscape pattern， showing temporal and spatial scale effects. On the time scale， indicators such as construction land， agricultural land， landscape dominance， aggregation， and diversity had significant correlations with various water quality parameters， and there was an inverse correlation in 2010 compared with that in other years for NH4+-N， TP， and TN. The landscape pattern in 2001 had the greatest explanation for water quality， with an explanation rate of 93.65%. The impact of greenland and woodland on water quality has begun to emerge in the past 10 years. ④ On the spatial scale， there were significant correlations between greenland and woodland， patch number， landscape shape index， diversity index， and water quality. There was a strong positive regulatory effect of greenland and woodland on NH4+-N， TP， and TN at the scale of 2 000 m. The patch number and landscape shape index had relatively strong regulatory effects on water quality on a larger spatial scale， whereas the Shannon diversity index had a better positive regulatory effect on water quality on a small scale. The landscape pattern within a buffer of 2 000 m had the highest interpretation degree for all factors， with an explanation rate of 68.47%. The study showed that rationally planning the proportion of greenland and woodland within the 2 000 m buffer zone and optimizing its landscape configuration is an important measure to purify the surface water quality of Suzhou Creek.

The Integrated Multi-satellitE Retrievals for the Global Precipitation Measurement (IMERG) provides new-generation satellite precipitation datasets with high spatio-temporal resolution and accuracy, which is widely applied in hydrology and meteorology. However, most examinations of the IMERG were conducted on daily, monthly, and annual scales, and inadequate research focused on the sub-daily scale. Thus, this study set up four sub-daily scales (1 h, 3 h, 12 h, and 24 h at 0.1° spatial resolution) and four spatial scales (0.1°, 0.25°, 0.5°, and 1° at 1 h temporal resolution) to finely evaluate the performance of IMERG products in the summer seasons from 2014 to 2019 over mainland China. The precipitation amount (PA), frequency (PF), and intensity (PI) were adopted to assess the performance of the IMERG referenced by the ground-based precipitation product of the China Meteorological Administration (CMA). The results show that the IMERG can capture the spatial patterns of precipitation characters over mainland China, but the PA and PI are overestimated and the PF is underestimated, and the evaluation results are highly sensitive to the different temporal and spatial resolutions. Compared with fine spatio-temporal scales, the performance of the IMERG is significantly improved when scaled up to coarser scales. Moreover, the IMERG shows a better performance of PA and PI in larger regions and during longer periods. This study provided a reference for the application of IMERG products in different spatial and temporal scales.

Ecosystem coupling: A unifying framework to understand the functioning and recovery of ecosystems

Flood hazard assessment of August 20, 2016 floods in Satna District, Madhya Pradesh, India

Microexplosions of light oil-water emulsified fuel droplets were successfully documented using a high speed video camera with laser illumination. The temperature profile and the local frequency of explosion occurrence were estimated in open spray flames of water-in-oil type emulsion formed using an air-assist atomizer with a set of ring pilot burners. The estimates of the local frequency of the explosion occurrence were made in the upstream region of spray flames, since their temperature profiles indicated that the heat release was accelerated in the upstream region from the nozzle tip up to the height of 80 mm. Microexplosions were frequently observed in the upstream region where no microexplosion phenomenon was observed in the former study. In addition, all of those had very small spatial and temporal scales. It is probable that the principal factor having effects on the heat release of emulsion spray flame is not the microexplosions of larger droplets, as former theories predicted, but those of smaller ones. We, furthermore, observed the microexplosions of smaller droplets using an ultra high speed video camera, the frame rate of which was 106 frames/s. It was observed that the smaller droplets, whose diameter were less than 50 μm, exploded in the spray flame and their temporal and spatial scales were around 10 μs and 300 μm, respectively.

<p>Multi-hazard events have the potential to cause damages to infrastructures and people that may differ greatly from the associated risks posed by singular hazards. Interrelations between natural hazards also operate on different spatial and temporal scales than single natural hazards. Therefore, the measure of spatial and temporal scales of natural hazard interrelations still remain challenging. The objective of this study is to refine and measure temporal and spatial scales of natural hazards and their interrelations by using a spatiotemporal clustering technique. To do so, spatiotemporal information about natural hazards are extracted from the ERA5 climate reanalysis. We focus here on the interrelation between two natural hazards (extreme precipitation and extreme wind gust) during the period 1969-2019 within a region including Great Britain and North-West France. The characteristics of our input data (i.e. important size, high noise level) and the absence of assumption about the shape of our hazard clusters guided the choice of a clustering algorithm toward the DBSCAN clustering algorithm. To create hazard clusters, we retain only extreme values (above the 99% quantile) of precipitation and wind gust. We analyse the characteristics (eg., size, duration, season, intensity) of single and compound events of rain and wind impacting our study area. We then measure the impact of the spatial and temporal scales defined in this study on the nature of the interrelation between extreme rainfall and extreme wind in the UK. We therefore demonstrate how this methodology can be applied to a different set of natural hazards.</p>

Single cell studies increasing reveal myriad cellular subtypes beyond those postulated or observed through optical and fluorescence microscopy as well as DNA sequencing studies. While gene sequencing at the single cell level offer a path towards illuminating, in totality, the different subtypes of cells present, the technique nevertheless does not offer answers concerning the functional repertoire of the cell, which is defined by the collection of RNA transcribed from the genome. Known as the transcriptome, transcribed RNA defines the function of the cell as proteins or effector RNA molecules, while the genome is the collection of all information endowed in the cell type, expressed or not. Thus, a particular cell state, lineage, cell fate or cellular differentiation is more fully depicted by transcriptomic analysis compared to delineating the genomic context at the single cell level. While conceptually sound and could be analysed by contemporary single cell RNA sequencing technology and data analysis pipelines, the relative instability of RNA in view of RNase in the environment would make sample preparation particularly challenging, where degradation of cellular RNA by extraneous factors could provide a misinterpretation of specific functions available to a cell type. Hence, RNA as the de facto functional molecule of the cell defining the proteomics landscape as well as effector RNA repertoire, meant that RNA transcriptomics at the single cell level is the way forward if the goal is to understand all available cell types, lineage, cell fate and cellular differentiation. Given that a cell state is defined by the functions encoded by functional molecules such as proteins and RNA, single cell RNA sequencing offers a larger contextual basis for understanding cellular decision making and functions, for example, proteins are increasingly known to work in concert with RNA effector molecules in enabling a function. Hence, providing a view of the diverse cell types and lineages present in a body, single cell RNA sequencing is only hampered by the high sensitivity required to analyse the small amount of RNA available in single cells, as well as the perennial problem of RNA studies: how to prevent or reduce RNA degradation by environmental RNase enzymes. Ability to reduce RNA degradation would provide the cell biologist a unique view of the functional landscape of different cells in the body through the language of RNA.

Surface albedo has been documented as one of the Essential Climate Variables (ECV) of the Global Climate Observing System (GCOS) that governs the Earth's Radiation Budget. The availability of surface albedo data is necessary for a comprehensive environmental modelling study. Thus, both temporal and spatial scale issues need to be rectified. This study reports about the availability of surface albedo data through in-situ and remote sensing satellite observations. In this paper, we reviewed the existing models for surface albedo derivation and various initiatives taken by related environmental agencies in order to understand the issues of climate with respect to surface albedo. This investigation evaluated the major activities on albedo-related research specifically for the retrieval methods used to derive the albedo values. Two main existing albedo measurement methods are derived through in-situ measurement and remotely sensed observations. In-situ measurement supported with number of instruments and techniques such aspyrheliometers, pyranometers and Baseline Surface Radiation Network (BSRN) and remotely sensed observations using angularly integrated Bi-directional Reflectance Distribution Function (BRDF) by both geostationary and polar orbit satellites. The investigation results reveals that the temporal and spatial scaling is the major issues when the albedo values are needed for microclimatic study, i.e. high-resolution time-series analyses and at heterogeneity and impervious surface. Thus, an improved technique of albedo retrieval at better spatial and temporal scale is required to fulfil the need for such kind of studies. Amongst many others, there are two downscaling methods that have been identified to be used in resolving the spatial scaling biased issues: Smoothing Filter-based Intensity Modulation (SFIM) and Pixel Block Intensity Modulation (PBIM). The temporal issues can be resolved using the multiple regression techniques of land surface temperature, selected air quality parameters, aerosol and daily skylight.

Considerable evidence suggests that cancer stem-like cells (CSCs) are critical in tumor pathogenesis. Though functional CSCs can be identified using dish-based tumorsphere assays, it is difficult to handle and monitor single cells in a dish-based format. Tumor-stromal interaction is another key regulator of cancer micro-environments, affecting tumorigenesis and metastasis. To enable tumorsphere assays that incorporate interaction with stromal cells, we developed a microfluidic dual adherent/suspension co-culture device. This device combined a suspension environment for single-cell tumorsphere assay and an adherent environment for co-culture of stromal cells in close proximity by selectively patterning polyHEMA in indented microwells. By minimizing dead volume and improving cell capture efficiency, the presented platform allowed the use of small samples (<100 cells), affording the potential to study rare cells such as circulating tumor cells (CTCs). As a proof-of-concept, we co-cultured single T47D breast cancer cells and primary cancer associated fibroblasts (CAF) on-chip for 14 days to monitor sphere formation and growth. Compared to mono-cultured T47D cells, co-cultured T47D have significantly higher tumorigenic potential (sphere formation rate) by three times and proliferation rates (larger sphere size). In addition to the phenotypic observation, the platform allows the retrieval of mono-cultured and co-cultured spheres for downstream analyses. Multiplexed single-cell gene expression analyses using C1 and BioMark HD platforms were performed to compare the expression of 96 target genes in co-cultured and mono-cultured T47D cells. Co-cultured cells expressed significantly higher MKI67, which suggests a possible mechanism for the elevated proliferation rate. Additionally, lower BAX (pro-apoptotic marker) expression matches well with higher sphere formation rate in the co-cultured cells. Interestingly, we noticed the down-regulation of CDH1, KRT8, and KRT18 in the co-cultured cells, indicating possible epithelial-mesenchymal transition induced by CAF. Single cell resolution, while to comparing between groups, also allows examination of cellular heterogeneity within one population. While cells in the mono-cultured group were more homogeneous co-cultured cells displayed clear bimodal gene expression distribution including, ANXA3, MTOR, MKI67, BAX, and PGR. This is suggestive of variable responses to the same stimuli at the single cell level. Combining the dual adherent/suspension co-culture platform presented here with the single cell gene expression analysis, we may successfully identify functional CSCs, investigate the phenotypic and transcriptional effects induced by tumor-stromal interactions, and study cellular heterogeneity in greater detail. Citation Format: Yu-Chih Chen, Shamileh Fouladdel, Zhixiong Zhang, Ebrahim Azizi, Euisik Yoon, Max S. Wicha. Single cell dual adherent-suspension co-culture microenvironment for studying tumor-stromal interactions in breast cancer stem cells. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4076.