JoVE Neuroscience is a multidisciplinary section devoted to investigations of the structure, function, physiology, and pathophysiology of the brain and nervous system. Included methodologies range from molecular and cellular level studies to full central and peripheral neural systems. Potential treatment platforms and surgical techniques for neurological diseases and disorders are also presented in this section.

Neuroscience

JoVE Medicine serves as a connection between basic research and clinical applications. Articles may present medical procedures, case studies or clinical trial methodologies. Included studies are often modeled towards predictive, preventative, personalized, and practical approaches to treatment of disease. The goal of research methodologies in this section is to improve overall patient care and prognosis.

Medicine

JoVE Immunology and Infection includes content from a variety of fields working toward a shared initiative of improving global health. Techniques evaluating the biological response to pathogens from the molecular to organismal level are presented as well as therapeutic agents and their efficacy in treating disease.

Immunology and Infection

JoVE Genetics publishes video articles demonstrating experimental approaches to investigate gene function and regulation. This includes methods to study gene expression, mutagenesis, epigenetics, genetic determinants of development, genetic disorders, population genetics and evolution.

Genetics

JoVE Environment is dedicated to research methodologies that address environmental concerns and seek to better understand Earth's ecosystem.  Special consideration is given to experimental methodologies that assess society’s impact on the environment, suggest solutions for protecting Earth’s resources, and develop sustainable fuel sources. Moving towards an environmentally conscious planet is a collaborative effort with contributions from both life and physical scientists.

Environment

JoVE Engineering encompasses a broad range of experimental and instrumental techniques utilized in physics research. Investigations in this area strive to address and answer a broad range of scientific questions, such as device mechanisms and efficiencies, using physical tools. This approach often requires a combination of specialties, and research in this area tends to be interdisciplinary with contributions from mechanical, electrical, and chemical engineers.

Engineering

JoVE Developmental Biology publishes research methodologies in the field of developmental biology. This includes methods that are used to study biological development in vitro and in vivo at the molecular, cellular, tissue, organ and whole organism levels.

Developmental Biology

JoVE Chemistry surveys a broad scope of chemical disciplines. This collection includes fundamental and applied research that investigates molecular interactions, properties, and structure spanning in the following core divisions: analytical, organic, organometallic, inorganic, bioinorganic, and biochemistry. This section also includes the design and preparation of materials and small molecules for advanced or unique applications.

Chemistry

JoVE Cancer Research illustrates experimental approaches in biomedical research and clinical practice aimed at understanding, detecting, treating and preventing cancer. The video articles in this section demonstrate methods to study the cellular and molecular mechanisms of cancer, animal models of cancer research, development of new therapies and diagnostics, tumor imaging, chemical and radiation treatments, surgical procedures and improvements in therapy. These video articles offer researchers and clinical practitioners an efficient way to learn the technologies and experimental methods in cancer research.

Cancer Research

JoVE Biology welcomes all general biology research methodologies. Content in this section canvases all fields of cell, molecular, and organismal biology, ranging from new applications of standard techniques to novel approaches aimed at understanding the functions of life and living organisms. This diverse section includes, but is not limited to, techniques in physical biology, cellular biochemistry, genetics, physiology, systems biology and a combination of eukaryotic and prokaryotic model systems.

Biology

JoVE Bioengineering merges both physical and life sciences to understand and predict biological processes. Applying physical science tools to life science questions allow for the discovery of better technologies to measure, diagnose, and clinically treat disease.

Bioengineering

JoVE Biochemistry publishes experiments that investigate the structure, function, and interactions of biological molecules. The video articles in this section demonstrate methods to study nucleic acids, proteins, carbohydrates and lipids as well as enzyme function, protein folding, molecular interactions and biochemical reactions.

Biochemistry

JoVE Behavior documents observational and experimental techniques that seek to understand human and animal behavior. Work in this field includes analysis of genetic causes and physiological responses to internal or external stimuli as well as the implicated brain regions.

Behavior

Coexistence theory has often treated environmental heterogeneity as being independent of the community composition; however biotic feedbacks such as plant-soil feedbacks (PSF) have large effects on plant performance, and create environmental heterogeneity that depends on the community composition. Understanding the importance of PSF for plant community assembly necessitates understanding of the role of heterogeneity in PSF, in addition to mean PSF effects. Here, we describe a protocol for manipulating plant-induced soil heterogeneity. Two example experiments are presented: (1) a field experiment with a 6-patch grid of soils to measure plant population responses and (2) a greenhouse experiment with 2-patch soils to measure individual plant responses. Soils can be collected from the zone of root influence (soils from the rhizosphere and directly adjacent to the rhizosphere) of plants in the field from conspecific and heterospecific plant species. Replicate collections are used to avoid pseudoreplicating soil samples. These soils are then placed into separate patches for heterogeneous treatments or mixed for a homogenized treatment. Care should be taken to ensure that heterogeneous and homogenized treatments experience the same degree of soil disturbance. Plants can then be placed in these soil treatments to determine the effect of plant-induced soil heterogeneity on plant performance. We demonstrate that plant-induced heterogeneity results in different outcomes than predicted by traditional coexistence models, perhaps because of the dynamic nature of these feedbacks. Theory that incorporates environmental heterogeneity influenced by the assembling community and additional empirical work is needed to determine when heterogeneity intrinsic to the assembling community will result in different assembly outcomes compared with heterogeneity extrinsic to the community composition.

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Experimental Protocol for Manipulating Plant-induced Soil Heterogeneity

Coexistence theory has often treated environmental heterogeneity as being independent of the community composition; however biotic feedbacks such as ...

The biological impact of microplastic pollution in human food and water sources is largely unknown, and drinking water sources are not exempt from this microplastic contamination. Here, we demonstrate a streamlined approach for capturing, quantifying, and identifying microplastics in drinking water. We present an analytical workflow termed the Silicon Nanomembrane Analysis Pipeline (SNAP) that takes advantage of novel Silicon nitride nanomembranes that enable a significant "concentration factor," which consolidates suspended particles into a planarized observation area for individuated, quantifiable, and multimodal particle analysis on the same substrate. SNAP's primary advantages derive from its use of ultrathin, Silicon nitride-based membranes housed in conventionally sized filter disks, enabling the direct capture and analysis of polymeric MPs on a non-polymeric background. Drinking water samples sourced in the Rochester, NY region, were collected from residential tap sources and analyzed using SNAP. Particles in each sample were characterized by optical and scanning electron microscopy (SEM), Raman spectroscopy, and energy-dispersive X-ray spectroscopy (EDX), and various identified constituents were quantified in proportion to the total captured particles.

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Multimodal Analysis of Microplastics in Drinking Water using a Silicon Nanomembrane Analysis Pipeline

The biological impact of microplastic pollution in human food and water sources is largely unknown, and drinking water sources are not exempt from this ...

Accurate estimation of drainage discharge (flow rate or water volume per unit time) is essential for calculating nutrient loads delivered to surface water and assessing the performance of edge-of-field conservation practices. Determining drainage flow rates requires monitoring the head in a drainage control structure and applying an appropriate equation for the weir installed in the structure. Previous studies that developed calibrated equations for weirs in control structures have produced different equations (i.e., different weir flow equation coefficients) for the same type of weir and control structure size. This study describes procedures for setting up experimental water flow rate and head measurements within a drainage control structure and developing a weir equation for flows contained within a V-notch weir. Additionally, the procedure for obtaining a weir equation for overtopping flows -- when the water level exceeds the top of the V-notch weir -- is outlined. This process involves using the weir equation developed in the laboratory for a V-notch weir and an online tool, the &#34;Weir Flow Equation Coefficients Calculator&#34;, developed by the authors. The online tool can also generate weir flow equation coefficients for both V-notch-contained and overtopping flows across various sizes of Agri Drain water control structures, even when users lack site-specific flow rate vs. head relationship.

parameterizing-v-notch-weir-equations-for-flow-monitoring-drainage

Parameterizing V-notch Weir Equations for Flow Monitoring in a Drainage Control Structure

Accurate estimation of drainage discharge (flow rate or water volume per unit time) is essential for calculating nutrient loads delivered to surface water ...

Oil sands process-affected water (OSPW), a by-product of bitumen extraction through surface mining in Alberta, Canada, contains various constituents of concern, including naphthenic acid fraction compounds (NAFCs). These organic compounds are particularly worrisome due to their toxicity and persistence in the environment. Constructed wetland treatment systems (CWTS) use plants and their associated microbes to attenuate contaminants in wastewater. Field-scale CWTS have been presented as a potential large-scale treatment option for OSPW, specifically for degrading NAFCs. To optimize the use of CWTS for large-scale treatment of NAFCs in OSPW, it is essential to deepen our understanding of various design parameters and explore ways to enhance efficacy.
Mesocosm-scale experiments serve as a valuable intermediary, bridging the gap between complex field trials and controlled laboratory settings. Mesocosms provide a controlled, replicable environment to study the effects of various parameters such as substrate, plant species, temperature, and retention time while incorporating ecological complexities in their design. Published and previous work has shown that this method is successful in evaluating the impacts of different parameters on the efficacy of CWTS to attenuate NAFCs in OSPW. This protocol outlines the design and setup of a surface flow wetland mesocosm, along with the experimental approach for treating NAFCs in OSPW. This method can be adapted to treat other wastewaters across diverse geographical locations.

mesocosm-scale-constructed-wetland-design-for-wastewater-treatment

Mesocosm-Scale Constructed Wetland Design for Wastewater Treatment

Oil sands process-affected water (OSPW), a by-product of bitumen extraction through surface mining in Alberta, Canada, contains various constituents of ...

Digital imaging and processing technology have evolved to facilitate the expansion of large-area imaging surveys, which increase our capacity to study the status, trends, and dynamics of organisms living in subtidal habitats. By creating photo-realistic digital twins for ex situ analyses, these approaches allow small field teams to collect substantially more data than was previously possible. Here we present a four-step, large-area imaging survey pipeline and analysis methodology, including image collection, model construction, ecological analysis, and data curation, that has been developed and refined through experimentation over the past decade. Each step described has a consistent focus on the unique value of the original source imagery. While types of data extracted from large-area image surveys are vast, we include here workflows to extract ecological data for structural complexity, community composition, and demographic analyses valuable for monitoring and hypothesis-driven efforts. We additionally include recommendations for metadata standards, which complement the collection of large-area imaging data and support archival efforts facilitating transparency and collaboration between research groups.

measuring-structure-composition-change-underwater-environments-with

Measuring the Structure, Composition, and Change of Underwater Environments with Large-area Imaging

Digital imaging and processing technology have evolved to facilitate the expansion of large-area imaging surveys, which increase our capacity to study the ...

Coastal wetlands are the largest biotic source of methane, where methanogens convert organic matter into methane and methanotrophs oxidize methane, thus playing a critical role in regulating the methane cycle. The wetlands in South Texas, which are subject to frequent weather events, fluctuating salinity levels, and anthropogenic activities due to climate change, influence methane cycling. Despite the ecological importance of these processes, methane cycling in South Texas coastal wetlands remains insufficiently explored. To address this gap, we developed and optimized a method for detecting genes related to methanogens and methanotrophs, including mcrA as a biomarker for methanogens and pmoA1, pmoA2, and mmoX as biomarkers for methanotrophs. Additionally, this study aimed to visualize the spatial and temporal distribution patterns of methanogen and methanotroph abundance utilizing the geographic information system (GIS) software ArcGIS Pro. The integration of these molecular techniques with advanced geospatial visualization provided critical insights into the spatial and temporal distribution of methanogen and methanotroph communities across South Texas wetlands. Thus, the methodology established in this study offers a robust framework for mapping microbial dynamics in wetlands, enhancing our understanding of methane cycling under varying environmental conditions, and supporting broader ecological and environmental change studies.

visualizing-methane-cycling-microbial-dynamics-in-coastal-wetlands

Visualizing Methane-Cycling Microbial Dynamics in Coastal Wetlands

Coastal wetlands are the largest biotic source of methane, where methanogens convert organic matter into methane and methanotrophs oxidize methane, thus ...

A method to recover and quantify micro- and nano-plastics (MPs and NPs) formed in the soil during biodegradation is needed to accurately assess the degradation and environmental impact of biodegradable plastic products. The presence of MPs and NPs in soil may alter soil properties like aggregation behavior or have toxic effects on soil biota. Existing MP recovery methods are not always suitable for measuring biodegradable polymers like polybutylene adipate terephthalate (PBAT); some common digestion procedures with acids or oxidizers can destroy PBAT-based biodegradable MPs. Identification methods like micro-FTIR and micro-Raman spectroscopy are also limited by the minimum size of particles that can be recovered and analyzed. Therefore, this method was developed to extract and quantify PBAT from soil to assess the mass fraction of MPs and NPs in the soil without chemically transforming PBAT. In the protocol, a chloroform-methanol solution is used to selectively extract PBAT from the soil. The solvent is evaporated from the extract, and then the extract is redissolved in deuterated chloroform. The extract is analyzed by proton nuclear magnetic resonance spectroscopy (1H-QNMR) under quantitative parameters to quantify the amount of PBAT in each sample. Solvent extraction efficiencies for PBAT range from 76% in a shady loam soil to 45% in an Elkhorn sandy loam soil. PBAT recovery may be reduced for photo-oxidized materials compared to pristine ones and may be reduced in soils with high clay content. Extraction efficiencies do not depend on PBAT concentration within the test range, but lower extraction efficiencies were observed for NPs than for MPs. PBAT quantification results were comparable to the quantification of plastic degradation by measuring cumulative soil respiration in a laboratory incubation study.

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Quantification of Polybutylene Adipate Terephthalate-based Micro- and Nano-plastics from Soil Using Proton Nuclear Magnetic Resonance Spectroscopy

A method to recover and quantify micro- and nano-plastics (MPs and NPs) formed in the soil during biodegradation is needed to accurately assess the ...

The global loss of biodiversity has motivated many studies that experimentally vary plant species richness and examine the consequences for ecosystem functioning. Such experiments generally show a positive relationship between above- and below-ground biodiversity and the functioning of terrestrial ecosystems. Moreover, this relationship tends to strengthen over time, seen as enhanced functioning of diverse plant communities and reduced functioning of low-diversity plant communities. Differences in multitrophic community assembly and biotic interactions in high- versus low-diversity plant communities are hypothesized to affect plant performance by altering consumer community structure and function and driving plastic or micro-evolutionary responses of plant species in the plant communities. To resolve this complex interplay of community history, we separated these effects into plant and soil history. Plant history refers to all plant-level responses to past abiotic and biotic selection pressures experienced in their communities, while soil history relates to all abiotic and biotic soil properties developed as a legacy of plant-soil interactions under variable plant diversity. We set up a biodiversity experiment in an Ecotron, a terrestrial mesocosm facility that allows controlling environmental conditions above- and below-ground, to test whether the strengthening biodiversity-ecosystem functioning relationship is due to soil history, plant history, or a combination of both. We established a plant diversity gradient consisting of 1, 2, 3, and 6 grassland plant species and factorially nested with soil history and plant history treatments for each level of plant species richness. Representative results demonstrate the successful establishment of target treatments in the Ecotron experiment, observing the effects of plant and soil history on initial plant development and final plant growth. Additionally, we provide a case study for data analysis of individual response variables. We outline research objectives and methods to comprehensively assess the multifunctional responses to the experimental treatments necessary to ultimately address the overarching hypothesis.

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JenaTron - An Experimental Approach to Study the Effects of Plant History and Soil History on Grassland Ecosystem Functioning

The global loss of biodiversity has motivated many studies that experimentally vary plant species richness and examine the consequences for ecosystem ...

The study aims to assess the effectiveness of microwave treatment (MWT) at a frequency of 2.45 GHz and a power of 800 W to control Japanese knotweed (Reynoutria japonica Houtt.) using a self-propelled device that was built in the in-house facility. The MWT was applied in the field population of knotweed in July 2022. First, plants were mechanically moved from the area of 1 m2, and next, the cut shoots around 4 cm high were microwave-treated for 25 min, 20 min, and 15 min. The control treatments were: 1) only cut plants and 2) rhizomes dug out to 30 cm deep. The effectiveness of the microwave treatments was observed for the next 11 months by counting the number of newly grown shoots. The results showed that a 25 min MWT was 100% effective in Japanese knotweed loss of vitality, while a 15 min MWT microwave treatment stimulated plant growth by around 50%, compared to controls. Rhizomes were dug out in a separate in vitro experiment for laboratory testing. The rhizomes were categorized by thickness and subjected to a 60 s MWT using a commercial microwave, after which their temperature and vitality were assessed. The temperature of rhizomes following MWT depended on their thickness. Those rhizomes that warmed to temperatures above 42 &#176;C were effectively destroyed. Summing up, the time plants are exposed to microwaves plays a major role in the effectiveness of this method. The longer the exposure to MWT, the better control. The thinner the rhizomes, the more effective the in vitro MWT rhizomes disposal.

control-disposal-invasive-japanese-knotweed-reynoutria-japonica-houtt

Control and Disposal of Invasive Japanese Knotweed Reynoutria japonica Houtt. Using Microwave Treatment

The study aims to assess the effectiveness of microwave treatment (MWT) at a frequency of 2.45 GHz and a power of 800 W to control Japanese knotweed ...

Derivatization and Separation of Barley Flour Metabolites into Four Fractions

Climate change increases drought risk to agriculture and impacts both food nutrient content and overall food security. Metabolomics is one way to observe and quantify the impacts of drought on grain and other agricultural products. The identified metabolites may allow for the identification of the biochemical response that allows the plant to tolerate stressful environments. The methodology presented herein allowed for the total metabolomic analysis of barley flour using gas chromatography/mass spectrometry (GC/MS). 
Barley flour metabolite extracts were fractionated into four fractions based on polarity. To allow for analysis by GC/MS, metabolites were derivatized to increase volatility and metabolite separation: fatty acids esters were derivatized into fatty acid methyl esters; sugars were oximated into their straight chain form; and metabolites with hydroxyl groups were converted to their corresponding silyl ethers. The derivatized samples were injected into the GC/MS and the generated mass spectra were used for metabolite identification by comparing the generated spectra to the National Institute of Standards and Technology (NIST) Tandem Mass Spectra library. The method described here can also be used to examine the total metabolome for other plants, furthering our understanding of the biochemical responses of stressed plants.

metabolomic-analysis-of-barley-by-gas-chromatographymass-spectrometry

Metabolomic Analysis of Barley by Gas Chromatography/Mass Spectrometry

Climate change increases drought risk to agriculture and impacts both food nutrient content and overall food security. Metabolomics is one way to observe ...

Journal - environment