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Corn (Zea mays) is an essential global crop, producing billions of bushels per year for food, feed, fiber, and fuel production. Field preparation and planning for planting maize are essential to the success of spring planting and an equally successful summer growing season. This protocol is aimed to help the researcher with field preparation, organizing the field before planting, hand planting, machine planting, and early season field assessments (i.e., scouting). When growing corn in the greenhouse or growth chamber, procedures may differ, especially regarding pest control, watering, and fertilization practices. This protocol serves as a guide based on organizing a maize nursery for research purposes and may slightly differ based on available machinery and weather conditions.

To understand what drives an immune response, it is important to characterize, at a molecular level, the site(s) on an immunogenic antigen that is directly contacted by a soluble antibody or B-cell antigen receptor (BCR) on the surface of a B lymphocyte. Moreover, antibody binding interactions with a microbial protein can interfere with the functional activity of a toxin (i.e., neutralization) and/or can aid in the clearance of the microbial protein from the body, further underscoring the importance of such characterization. Phage display technology is a potent tool that can be used to study any type of protein-protein interaction. In recent years, we have refined methods for the identification of the minimal binding contact sites of an antibody with an antigen. Here, we describe a workflow for optimizing antibody-mediated selection and for the identification and characterization of antigen-specific epitopes. This workflow includes (1) the generation of large libraries of random fragments of a gene of interest cloned into the validated pComb-Opti8 phagemid expression cloning vector system; (2) electroporation of these libraries into electrocompetent bacterial cells and subsequent recovery of viral particles, each of which displays the cloned gene fragment product as a fusion protein with the filamentous phage major coat protein VIII (pVIII); (3) recovery of individual phagemid clones that express the smallest functional epitopes recognized by an experimental antibody; (4) an efficient means of using high-throughput DNA sequencing to interrogate sequentially selected libraries to rapidly identify the gene subregions encoding epitopes of interest; and (5) means for the further characterization of potential antibody-epitope binding interactions.

Genetic toolsets are essential for gene discovery, elucidating biological pathways, and accelerating molecular breeding of superior crops in plant biology and agriculture. Among these, the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9) system has emerged as a powerful and indispensable tool for precise genome editing in maize (Zea mays L.). This protocol presents a comprehensive, maize-specific approach to constructing CRISPR vectors and analyzing transgenic plants carrying targeted gene mutations. It is organized into two major sections. The first section provides a step-by-step guide for designing guide RNAs and oligonucleotides (oligos) to construct CRISPR vectors containing one, two, four, or multiplexed (up to eight) single-guide RNAs (sgRNAs). It also describes the modular assembly of these sgRNAs with the Cas9 expression cassette using the Gateway cloning strategy to streamline vector construction. The second section focuses on genotyping CRISPR-edited plants by detecting and characterizing target mutations. Four complementary methods are outlined: (1) the T7 endonuclease I (T7EI) assay, (2) restriction enzyme digestion, (3) Sanger sequencing of PCR amplicons, and (4) high-throughput sequencing. Methods 1 and 2 offer rapid and cost-effective screening for small insertions or deletions (indels), while methods 3 and 4 provide high-resolution and scalable mutation analysis. Together, this workflow offers researchers an efficient, flexible, and reliable system for genome editing and mutation validation in maize, supporting both functional genomics studies and trait improvement applications.

The human immune system evolved to defend against the panoply of microbial threats. By harnessing such ability, vaccines have cumulatively saved hundreds of millions of lives. Despite such tremendous success, there have also been remarkable failures, such as the lack of a clinically proven vaccine against Staphylococcus aureus (SA), which continues to pose an urgent public health threat. In practice, it has proven challenging to identify the molecular basis for relevant epitopes for this pathogen. Here, we summarize our experience implementing an integrated approach using phage display technology for the identification of B-cell epitopes of microbial virulence factors, which we developed with a focus on SA. This approach was used to define minimal B-cell epitopes of the staphylococcal leucocidin family of pore-forming toxins (PFTs) that have been implicated in staphylococcal clinical infection. Our methodology provides proof of principle for an approach well suited for the rapid and efficient generation of modular protein-based vaccines for protection from clinical infection, which can be used to target pathogens for which no vaccine is currently available.

In maize, abundant pollen production and easy controlled pollination permit the direct mutagenesis of pollen to produce populations of independent mutant lines. Pollen can be treated with alkylating agents, such as ethyl methanesulfonate (EMS), to induce point mutations. The ease of applying and decontaminating this mutagen after the mutagenesis application and the advantages provided by the mutation spectra for subsequent bioinformatic analysis make EMS an attractive mutagen. We provide a maize pollen mutagenesis protocol with a list of critical supplies, a step-by-step procedure, and troubleshooting tips. Pollen is freshly collected and suspended in an emulsion of EMS and paraffin oil. The slurry of pollen, oil, and EMS is then directly placed on prepared maize silks to perform pollinations. Mutations result during embryogenesis due to replication-dependent mispairing at alkylated residues contributed by sperm nuclei. Thus, each seed bears an independent set of mutations. These progenies can be analyzed directly, as is the case in targeted mutagenesis experiments or the exploration of dominant genetic variation. Alternatively, the progenies of self-pollinated plants can be screened in the next generation to discover novel recessive mutations. In addition to the dose of EMS and contact time, the genetic background of maize can significantly influence outcomes, and some optimization of dose and contact time may be required for a genetic background and specific use case. Although we outline good practices for safe handling of EMS and waste, researchers should consult their local safety officers to ensure safe handling, decontamination, and disposal of EMS, which is toxic.

Understanding how the auxin hormone signaling pathway components come together to orchestrate cellular responses is key to engineering the growth and development of maize. Although a variety of techniques exist to measure auxin activities in plants, many are time- and resource-intensive or do not easily allow for high-throughput quantitative measurement of component libraries. The AuxInYeast system is a synthetic biology tool that facilitates complex biochemical analysis of the auxin hormone signaling pathway from essentially any plant. AuxInYeast uses Saccharomyces cerevisiae yeast as a heterologous expression platform for auxin signaling pathway components with fluorescent tags that facilitate measurement of auxin perception, repression, and activation. This protocol describes how to use fluorescence flow cytometry for these AuxInYeast experiments. As a case study, we focus on AuxInYeast strains built to measure maize auxin perception (i.e., those that express receptors and fluorescently tagged repressors that degrade upon auxin exposure). This protocol describes two different types of cytometry assays. The Steady-State Assay measures the extent of auxin-induced repressor degradation at one or two time points across many AuxInYeast strains and is particularly useful for initial assessment of whether auxin-induced degradation occurs and for dose response assays. The Time-Course Assay is used to measure auxin-induced repressor degradation dynamics over 2-3 h in a smaller number of strains. It is most useful for assessing the range of degradation rates across sets of repressors or receptors, and to precisely determine the impact of mutations and natural variation on degradation rate.

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Synthetic biology approaches merge the tenets of engineering with established biological techniques to answer fundamental questions about living systems and to engineer biological forms and functions. Following the engineering principle of design-build-test-iterate, this review serves as a guide to applying synthetic principles and approaches in maize. We outline strategies for (1) choosing the optimal model organism to serve as a heterologous chassis for maize signaling pathways, (2) designing and building biological parts and devices to express pathway components, (3) choosing an analytical technique to measure pathway function, and (4) optimizing and troubleshooting the designed system. Auxin is a hormone that is essential for plant growth and development, regulating cellular proliferation and differentiation. Considering the importance of auxin for maize development in aerial and underground tissue, it was an obvious starting point for synthetic biology approaches. We use the maize nuclear auxin response recapitulated in yeast (AuxInYeast) system to showcase the power of heterologous expression approaches for testing fundamental attributes of the evolution, genetics, and biochemistry of signaling pathways that may be challenging to assay in planta. This approach involves co-expression of maize auxin signaling components in Saccharomyces cerevisiae coupled with fluorescence flow cytometry to quantify signaling activity. We and others have used this system to interrogate the dynamics of pathway signaling, interactions between paralogous components, and the adaptation of auxin signaling over large evolutionary distances. Thus, the AuxInYeast system is a fast, high-throughput, hypothesis-generating platform that can be readily adapted by the maize community to creatively answer questions about fundamental maize biology and to drive development of novel tools for breeding and plant engineering.

Grain quality is defined as the suitability of grain for a particular use. It is usually designated by chemical composition or physical properties of the grain. The ability to measure grain quality is important for identity preservation of specialty grain market classes, for development of new varieties with improved quality through breeding, and for basic scientific studies on the genetic or biochemical control of grain quality traits. This review introduces official methods for measuring maize compositional traits, including protein, starch, oil, amino acid, phytate, and phosphorus content. Additionally, we discuss two nonofficial methods: measuring phytate and available phosphorus levels, and assessing amino acid balance. Phytate and available phosphorous impact the mineral nutrition of grain, while amino acid balance reflects the value of grain as a protein source and the bioavailability of protein. We also describe the use of near-infrared spectroscopy (NIRS) to assess levels of various compounds in maize. NIRS relies on the fact that compounds with differing molecular properties uniquely interact with the near-infrared region (750-2500 nm) of the electromagnetic radiation spectrum, and thus, generate spectral information that can be used to develop calibration models/equations for predicting the concentration of the compounds in grain samples. We discuss how sensitivity, accuracy, precision, throughput, and cost influence the choice of assay used to assess grain quality. Furthermore, we discuss how appropriate experimental design and data analysis can improve analytical outcomes when assessing grain quality.

Amino acids are important nutrients in maize grain used for food and feed. Because all 20 amino acids are required for growth and development, a deficiency in a single essential amino acid limits the utilization of dietary protein. In monogastric animals, 10 amino acids must be supplied by the diet and therefore are considered essential. The remaining amino acids can be made from the 10 essential amino acids. Lysine, tryptophan, and methionine are frequently limiting essential amino acids in grain-based diets. Therefore, increasing levels of limiting essential amino acids in grain is an important objective in crop improvement. Standard chromatographic methods for assessing levels of amino acids in grain are extremely accurate, but very expensive. Here, we present a protocol for high-throughput analysis of amino acids in grains, using microbial assays, conducted in 96 well plates, that can be carried out for a fraction of the cost of the standard chromatographic methods. We use Escherichia coli strains that have mutations in the biosynthetic pathway of the amino acid of interest. These strains are auxotrophic, so their growth is proportional to the amount of a specific amino acid in the media. The level of the amino acid of interest in a corn extract is determined by adding the corn extract to the microbial growth medium and measuring the growth of the culture as turbidity in a 96 well plate reader. This protocol is designed for analysis of methionine, but can be adapted for the analysis of any amino acid, by substitution of an appropriate auxotrophic strain of E. coli.

Squamates, the taxon that comprises lizards and snakes, are a diverse assemblage of reptiles represented by more than 11,000 described species. Studies of gene function in squamates, however, have remained very limited, largely due to the lack of established genetic tools and suitable experimental systems. A major challenge for the development of CRISPR-based gene editing in these reptiles is that the isolation of fertilized oocytes or single-celled embryos is impractical for most species, given that fertilization occurs internally, the females of many species can store sperm, and simple methods for detecting ovulation are lacking. To overcome these challenges, we have developed a unique surgical approach in the brown anole lizard Anolis sagrei The procedure enables users to access and microinject unfertilized oocytes while they are still maturing within the lizard ovary. We describe here the methods to anesthetize adult female anoles, access the ovary through a surgical incision into the coelomic cavity, and microinject unfertilized oocytes with CRISPR-Cas9 ribonucleoprotein complexes to generate targeted mutations, enabling the routine production of gene-edited lizards.

Maize is a globally important grain crop that is important for food and fuel. Northern corn leaf blight, caused by Exserohilum turcicum, is an important fungal foliar disease of maize that is highly prevalent and causes yield losses globally. Microscopy can be used to visualize plant-fungal interactions on a cellular level, which enables pathology and genetics studies. Host resistance and isolate aggressiveness can be characterized at different stages of disease development, which enables a more detailed understanding of the pathogenesis process and host-pathogen interactions. Our protocol outlines an efficient, cost-effective method for staining E. turcicum tissue on inoculated maize leaves and visualizing samples using a compound fluorescence microscope. This protocol uses KOH treatment followed by aniline blue staining, which stains glucans present in plant and fungal cell walls, and samples are visualized using fluorescence microscopy. Quantitative data about fungal structures including the conidia, hyphal structures, and appressoria, the structures formed to push through the plant leaf surface after conidia have germinated, can be obtained from the images generated using this technique. Visualization of these structures can help pathologists understand plant-pathogen interactions for maize and E. turcicum This method has advantages over other methods because the stain is less toxic than other available stains, samples can be processed in a more high-throughput manner than other protocols, and the required supplies are relatively inexpensive.

Phage display technology is enabled by genetic fusion of a foreign protein domain to a phage coat protein, without interfering with the phage's ability to replicate by infecting bacterial host cells. The displayed domain is exposed on the phage particle (virion) surface, where it can interact with molecules or other substances in the surrounding medium; in this regard, it acts like a normal protein. However, it possesses a superpower that is unavailable to ordinary proteins: It is easily replicated in great abundance because it is attached to a replicating virion whose genome includes its coding sequence. The main way this technology is exploited is construction of huge phage display "libraries," comprising billions of phage clones, each displaying a different protein domain, and each represented by thousands, millions, or billions of genetically identical virions-all mixed together in a single vessel. Surface display allows exceedingly rare virions whose displayed protein domains happen to bind a user-defined molecule or other substance-generically called the "selector"-to be isolated from such libraries by an affinity selection process. The yield of selector-binding virions is much too low to be of practical use, but their number is readily increased by many orders of magnitude by propagating the virions in host bacteria in culture. This overview is a critical review of recent developments of this technology. It does not review the entire arena of contemporary phage display; there is special emphasis on phage display's most prominent application, phage antibodies, in which the displayed domain is an antibody domain, and the selector is an antigen of interest.

Anolis lizards are an ecologically diverse group that includes more than 400 described species. These reptiles have been the subject of wide-ranging studies, from speciation and convergent evolution to climate adaptation and tail regeneration. While CRISPR-based gene editing has tremendous potential to reveal new insights into these and other aspects of Anolis biology, the reproductive biology of these reptiles has presented significant barriers to gene editing. Here, we briefly summarize gene editing approaches in vertebrates and discuss some of the major challenges associated with the performance of gene editing in anoles. We then introduce a recently established surgical procedure that enables the injection of CRISPR-Cas into the developing oocytes of female lizards. This approach circumvents the need to manipulate early-stage embryos and permits the production of gene-edited anoles. This method has recently been successfully adapted for use in other reptiles, suggesting that it may be effective in a wide range of species and will broadly enable studies of gene function in reptiles.

Zea mays (maize) is a globally important cereal crop and a key system for studying plant development and stress responses. Proteome profiling and phosphoproteome profiling provide direct, quantitative readouts of protein abundance and phosphorylation states, which offer insights into aspects of regulation and cellular function that transcript-level measurements alone cannot provide. Robust and reproducible methods are essential for generating accurate and biologically relevant data in proteomics studies. The complexity of plant tissues, however, poses challenges for developing reliable sample preparation workflows. Here, we describe a detailed sample preparation protocol for quantitative proteome and phosphoproteome profiling in maize. The protocol encompasses protein extraction, filter-aided sample preparation (FASP), peptide desalting, tandem mass tag (TMT)-based labeling for quantitative multiplexing, and complementary TiO2 and Fe-NTA enrichment steps, yielding peptides suitable for analysis by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). This approach enables the quantitative profiling of protein abundance and phosphorylation dynamics in maize tissues.

Maize is an important food and fuel crop globally. Ear rots, caused by fungal pathogens, are some of the most detrimental maize diseases, due to reduced grain yield and the production of harmful mycotoxins. Mycotoxins are naturally occurring toxins produced by certain fungal species that can cause acute and chronic health issues in humans and animals that consume mycotoxin-contaminated grain. Pathogens can infect the developing ear through silks, or through wounds in the ears produced by pests. Plants naturally develop genetic resistance to pathogens. The maize genes involved in resistance to the pathogen may be different, depending on whether the ear was infected via silks or wounds. To differentiate between these two forms of resistance, natural infections can be reproduced by injecting inoculum through the silk channel, or by producing wounds using a needle, and introducing inoculum directly onto developing ears. Our protocol describes a technique used to inoculate developing maize ears with Fusarium graminearum, one of the fungal species that causes ear rot. We describe both silk channel and side needle inoculation techniques. Our protocol uses a backpack inoculator for both methods of infection, allowing for high-throughput inoculations, which are necessary for large field experiments. After harvest, the ears are visually rated on a percentage of disease scale. The protocol results in quantitative data that can be used for research on elucidating genetic resistance to fungal pathogens to assist breeding selections, and to understand plant-pathogen interactions of ear rots in maize.

Harvest scheduling, seed drying, and good storage practices are essential for maize research to avoid negative impacts on the quality of the seeds and to maximize seed viability. Embryo growth and accumulation of energy reserves in the endosperm are completed ∼40 days after pollination, of which the last 10-20 days are devoted to maturation and desiccation. Seed maturity is affected by many factors including temperature, day length, humidity, and soil moisture. Once seeds are mature, they must be harvested. Hand harvesting, which allows for greater control and minimizes ear damage, is primarily used in genetic nurseries and general research because each genotype is represented by a small number of plants. Hand harvesting is also used where there is a mix of manually pollinated and undesired open pollinated ears, and can be a selective harvest depending on the research objectives. However, hand harvesting is more labor-intensive and time-consuming compared to combine harvesting. If harvesting a yield trial, where the purpose is to collect yield data and identify promising genotypes, the use of a combine (not described in this protocol) is critical to consistently capture grain weight, moisture, and test weight for each plot. Following harvest, materials must be dried to the appropriate moisture content before storage. Corn is typically stored using the "active collection" model, with temperatures set between 5°C and 10°C and low relative humidity. This harvest protocol is intended to assist laboratories that are new to maize research and may be modified based on project goals, genetic material, equipment, or available space.

Zea mays, also known as maize or corn, is a staple crop as well as a classical model organism for plant genetic studies and research. To conduct maize research, plants must be properly cultivated in field or greenhouse conditions to ensure reproductive success and safeguard genetic identity through controlled pollinations. Genetic studies require knowing which alleles or genetic combinations (genotype) are present in an individual so the geneticist can create new combinations or select the desired genotypes. In order to determine and maintain the genetic identity of a corn plant and make precise selections of male and female plants, reproductive structures must be covered and isolated prior to silking and anthesis, or pollen shed. Doing so allows experimenters to make controlled pollinations to produce the desired genotype. Successful pollination of corn requires proper field design and preparation, careful planting to maintain distinct genetic families, and careful monitoring of growth and husbandry followed by proper harvest and seed storage. These activities have been optimized over the past 100 years. In this review, we summarize each step needed to produce a generation of corn from planting to harvest.

Corn, or maize, is an economically important crop and frequently used model organism for genetic studies. Controlled pollinations are essential to the execution of these studies. This protocol outlines the basic steps in planning, setting up, and making manual pollinations. In addition, a method of extending pollen for multiple pollinations, as well as types of pollinations and their respective labeling schemes, are detailed. A troubleshooting guide is provided with solutions for common problems one might encounter when making manual pollinations. Although growing conditions and germplasm may cause slight deviations from this protocol, the basic principles can be applied to any corn research program.