Current Topics and Methods Courses
SPRING
Spring 2020
HCS 8830
Abiotic stress tolerance
Instructors: Kristin Mercer; mercer.97@osu.edu and Leah McHale; mchale.21@osu.edu
1 credit
7 Week 1
Class numbers: 35187 and 35188 (Wooster)
Meeting Days/Times: Thursdays 10:00 AM -12:00 PM
Location: Howlett 139 video-linked to Williams 123
The purpose of this journal club is:
- To better understand mechanisms of abiotic stress tolerance in plants.
- To differentiate between plastic responses and adaptations, whether inducible or canalized.
- To understand how researchers have explored the genetic basis of abiotic stress tolerance. Papers and discussions will emphasize these themes, especially within the context of agricultural plants and issues facing agriculture due to global change.
HCS 7806
Systems Approach Field Research
Insructor: Marília Chiavegato; chiavegato.1@osu.edu
1 credit
Class numbers: 33717 (Columbus), 33718 (Wooster)
Spring 2020 7 Weeks Session 2
Meeting Times: TH 10:20 AM - 12:20 PM
Location: 202F Kottman Hall video-linked to 123 Williams Hall
The goal of the course is to introduce students to holistic and systems approach field research. The differences between reductionistic and holistic research approaches will be explored. We will discuss research routine methods to deal with complex relationships within agroecosystems (plant-animal-soil-water-atmosphere). This course will provide students with the basic concepts of experimental design and data analysis in systems approach field experiments. To get the most out of this class students should have a course in basic statistical methods.
The main topics that will be covered are:
- Experimental design to test one-to-one relationships
- Isolating relationships from a complex context
- Disturbances in field and on-farm experiments
- The fragmentation of knowledge within experiments and institutions
- Short and long-term experiments
- Multidisciplinary, transdisciplinary and holistic studies
- Dealing with outliers and empirical deviations and the focus on averaged results
- Experimental design and statistical analysis in systems approach experiments
HCS 7806
Publishing in the Tri-Society Journals
Instructor: Laura Lindsey, lindsey.233@osu.edu
Credits: 1
Class number: 32931 (Columbus) and 32932 (Wooster)
Thursdays 1:50 PM - 2:50 PM
Location: Kottman Hall 202F and Williams 108 (Wooster)
The purpose of this methods course is to understand publishing guidelines of Tri-Society journals, including Agronomy Journal, Crop Science, Agricultural and Environmental Letters, and Crop, Forage, and Turfgrass Management, and produce a draft publication that will be submitted to one of these journals. Students should have data analyzed prior to taking this course.
HCS 7806
Introduction to concepts of Bayesian Statistics
Instructor: Jonathan Fresnedo, fresnedoramirez.1@osu.edu
Credits: 2
7-weeks session 2
Class numbers: 35390 (Wooster) and 35389 (Columbus)
Meeting time: Tuesdays and Thursdays, 2:30 PM; 2 hr lecture on Tuesday; 2 hr Lab on Thursday
Location(s): Williams 117A (Wooster) and Howlett 340 (Columbus)
This course will provide an overview about methods of Bayesian statistical inference. The class has a humble objective: that students learn (or are at least become aware) of the vocabulary, terminology and concepts regarding this type of statistical inference, which has increasingly grown in popularity in scientific literature. Explanations to the terms and concepts, as well as hands-on data processing will be included. Mathematical foundations will not be the core of the course; however, applications based on the analysis of datasets using JASP and R will be covered during the labs. The evaluation will be based on quizzes and preparing a glossary.
It is recommended that students interested in the class have already taken a course of basic statistical methods (experimental design is not necessarily but a course on descriptive statistics is required) and have some experience with the Statistical Language R.
The main topics that will be approached are:
- Refresh of probabilistic distributions
- Bayesian inference,
- Linear models
- Model comparison
- Application and introduction to Markov chain monte Carlo (MCMC)
- Introduction to categorical/count models
- Introduction to hierarchical models
Spring 2019
HCS 7806
Scientific Writing: publishing in peer-reviewed journals
Instructor: Michelle Jones, jones.1968@osu.edu
2 credit hours
Class numbers: 32837 (Columbus) and 32838 (Wooster)
Meeting time: MW 10:05 AM - 10:55 AM
Location: 202F Kottman Hall video-linked to 102 Gourley (Wooster)
This methods course will provide graduate students with an opportunity to improve their scientific writing skills. Students will also receive insight, and develop necessary skills that will assist them in navigating the scientific publishing process from start to finish. Students will have completed a manuscript final draft using their own research data by the end of the semester.
Course will be open to graduate students in Wooster and Columbus who have data that is ready to publish. Enrollment will be limited to 10 students. Students should contact the instructor to indicate interest and get permission to enroll.
Course objectives
- Students will learn how to better organize the results of their experiments and communicate them to the scientific community through publication in peer-reviewed journals.
- Students will improve their writing skills so that manuscript preparation becomes more efficient and productive.
- Students will learn how to successfully navigate a manuscript through the submission, peer-review, and publication process.
- Students will become more proficient at identifying the strengths and weaknesses of papers published in diverse scientific journals.
- Students will learn to become effective reviewers.
HCS 8830
Crop Mythbusters: What Works and What Doesn't
Instructor: Laura Lindsey, lindsey.233@osu.edu
7-week 2
Mondays 12:30 - 2:30 PM
The purpose of this current topics course is to introduce students to non-traditional farming practices they may encounter and to determine if these non-traditional practices are supported by the current literature.
Spring 2018
HCS 8830
Plant hormone signal transduction mechanism
Instructor: JC Jang, jang.40@osu.edu
7 Weeks
Topics of presentation: Abscisic Acid (ABA), Auxin, Brassinosteroids (BRs), Cytokinins (CKs), Ethylene, Gibberellins, Methyl Jasmonates, Peptide hormones, Salicylic Acid (SA), and Stringolactones.
Spring 2017
HCS 7806
Using Multimedia to Communicate Science to the Public
- Short videos communicating an aspect of plant science or food production
- Learn how to properly plan, execute, and edit videos
- Design an independent project and collaborate with other students’ projects
- Development of Ohio State’s Plant Breeding website:
- Invite relevant faculty
- Learn how to edit web content using Drupal
- Create web content for Ohio State’s Plant Breeding website
- Videos and infographics
- Educational pages about plant breeding/genetics
HCS 7806
Multivariate Methods using SAS and R
You should have taken a prior statistics class.
- Mon (lecture) 2-3pm; Mon (lab) 3-5pm, video-link to Wooster
- Howlett 139; Gourley 102
Students will need a laptop with SAS and/or R for the recitation
HCS 8830
Principles and Applications of Plant Hormone Signal Transduction Mechanisms
HCS 8830
Crop Mythbusters- What Works and What Doesn't
AUTUMN
Autumn 2019
HCS 7194
Genome Analytics
Instructor: Jonathan Fresnedo, fresnedoramirez.1@osu.edu
14-week, 3 credit hours
Meeting Time: Tuesday 1:50 PM – 2:45 PM and Thursday 1:50 PM - 4:35 PM
Locations: Selby 203, Wooster campus and Kottman 202f, Columbus campus
55 minutes lecture on Tuesday, 55 minutes lecture and 1:5 hr Lab on Thursday
Class Numbers: 34410/34411 for Columbus and 34740/34741 for Wooster
*Permission of the instructor required*
The goal of the Genome Analytics course is to facilitate a hands-on analytical and quantitative approach for graduate students to learn about the basic pipelines for the data analysis of genomic sequences, focusing on incorporating these bioinformatics pipelines into their research. This course provides students with the basic concepts for the subsequent broad survey of the latest advances and applications on topics related to genomic sciences and bioinformatics and their implementation in biological sciences, particularly ag-related disciplines. Students will have access to computing resources from the Ohio Supercomputer Center and GitHub repositories.
The main topics that will be approached are:
- Command line
- Introduction to the analysis of sequencing data
- Genome assembly
- Gene expression
- Variant calling
- Metagenomics and microbiomes
- Epigenetics
HCS 7806
Code Clues: Deciphering SAS Output
Instructor: Alex Lindsey, lindsey.227@osu.edu
14 weeks, 1 credit
Meeting Time: Wednesdays 12:40 -1:35 PM
Location: Kottman 112
Class numbers: 35586
Description: Students will gain experience looking through SAS code and output to discern where possible errors can be seen, as well as what measures can be done to address some of these issues. Emphasis will be placed on model development and output discernment for common field experimental designs, such as randomized complete block and split-plot RCBD. Students will be expected to build models for the class related to their experimental data and design, and gain experience in examining output tables to troubleshoot common issues with code construction and placement of terms in the model.
HCS 8830
Plant hormone signal transduction mechanism
Instructor: JC Jang; jang.40@osu.edu
7W1
Time/Location: TBA
Topics of presentation:
- Abscisic Acid (ABA)
- Auxin
- Brassinosteroids (BRs)
- Cytokinins (CKs)
- Ethylene
- Gibberellins
- Methyl Jasmonates
- Peptide hormones
- Salicylic Acid (SA)
- Stringolactones
Presentation format:
- Nature of this hormone (1 slide).
- History of this hormone (1 slide).
- Biosynthesis and metabolism of this hormone (1 to 2 slides).
- Functions of this hormone (1 to 2 slides). See examples of info via http://pages.wustl.edu/ipgsa/plant-hormones
- How this hormone signal is sensed and transmitted by plants. Select a recent research paper on the breakthrough of molecular/genetic mechanism of plant hormone signal transduction.
- Practical application of this particular plant hormone signal transduction mechanism.
Autumn 2018
HCS 7194
Genome Analytics
Instructor: Jonathan Fresnedo, fresnedoramirez.1@osu.edu
14 weeks, 3 credits
Meeting Time: Tuesday 1:50 PM – 2:45 PM and Thursday 1:50 PM - 4:35 PM
Location: Williams 117A and Selby 203, Wooster campus
Class Numbers: 35346-35347
55 minutes lecture on Tuesday, 55 minutes lecture and 1:5 hr Lab on Thursday
The Genome Analytics course is to facilitate a hands-on analytical and quantitative approach for graduate students to learn about the basic pipelines for the data analysis of genomic sequences, focusing on incorporating these bioinformatics pipelines into their research. This course provides students with the basic concepts for the subsequent broad survey of the latest advances and applications on topics related to genomic sciences and bioinformatics and their implementation in biological sciences, particularly ag-related disciplines. Students will have access to computing resources from the Ohio Supercomputer Center and GitHub repositories.
The main topics that will be approached are:
- Command line
- Introduction to the analysis of sequencing data
- Genome assembly
- Gene expression
- Variant calling
- Metagenomics and microbiomes
- Epigenetics
HCS 8830
Current Topics in Metabolomics
Instructor: Jessica Cooperstone, cooperstone.1@osu.edu
First 7-week session; 1 credit
Meeting time: Mondays 1:50 - 2:45 PM
Location: Parker 120 video-linked to 123 Williams
This journal club will focus on critically reviewing and evaluating recent publications in metabolomics, with a focus on applications in plants, foods and human health. The goals of this course are to increase student familiarity with reading and interpreting the metabolomics literature, and to understand ways in which metabolomics may be a useful approach to students’ research.
HCS 7806
Using Multimedia to Communicate Science to the Public
Instructor: Leah McHale, mchale.21@osu.edu
Second 7-week session; 1 credit
Meeting time: TBA
Class #: TBA
This course is aimed at graduate students seeking to further their science communication abilities. Primarily, students will work collaboratively to create multi-media content aimed at the general public and communicating a topic related to plant science or food production. There will be the opportunity to host these media on HCS websites including the departmental website and Ohio State’s Plant Breeding website.
Autumn 2017
HCS 7806
Introduction to concepts of Bayesian Statistics
This course will provide an overview about methods of Bayesian statistical inference. The class has a humble objective: that students learn (or are at least become aware) of the vocabulary, terminology and concepts regarding this type of statistical inference, which has increasingly grown in popularity in scientific literature. Explanations to the terms and concepts, as well as some hands-on data processing will be included. Calculations would not be the core of the course; however, the analysis of datasets using R, JAGS and Stan are going to be covered during the labs. The evaluation will be based on quizzes.
It is recommended that students interested in the class have already taken a course of basic statistical methods (experimental design is not necessarily but a course on descriptive statistics is required) and have some experience with the Statistical Language R.
The main topics that will be approached are:
- Refresh of probabilistic distributions
- Bayesian inference,
- Linear models
- Model comparison
- Application and introduction to Markov chain monte Carlo (MCMC)
- Introduction to categorical/count models
- Introduction to hierarchical models
HCS 7806
Small Plot Research Methods and Equipment
(Since we will be using equipment, the course will be Columbus only located off-campus at the Agronomy Shop)
Description: The purpose of this methods course is to discuss small plot research methods for agronomic crops. Students will learn about basic equipment maintenance, how the research equipment works, and have the opportunity to harvest soybeans and plant wheat.
Summer
Summer 2019
HCS 8830
Current research topics on controlled environment plant physiology and technology
Instructor: Chieri Kubota, kubota.1@osu.edu
1 credit
Class numbers: 20831, 21101
Meeting time: Tuesdays 9:10 - 10:10 AM
Location: Howlett 139 and 123 Williams (Wooster)
This room will be used for our first introduction meeting. After that, the usage will be minimum (only during the time we need to meet in person).
Online - Zoom connection (Zoom meeting will be up to two hours every other week: a total of 6 Zoom meetings will be scheduled for the course)
Students will review recent research publications in the areas of controlled environment crop production, with focus on plant physiology and controlled environment technology. Students will take turns and select papers with the intent to understand and evaluate the contents analytically. Then students will synthesize the information to present to other peer students in the course and also develop a corresponding impact statement of the finding to better communicate with the relevant industry stakeholders. The goal of this course is to get the most up-to-date understanding of the controlled environment crop physiology research and communicate the impact effectively in a public space.
Course learning outcomes
- Become familiar with the current research status of applied plant physiology under controlled environment
- Become familiar with the current and potential technological applications of applied plant physiology under controlled environment
- Develop skills of analytical thinking through evaluating methods and results reported in peer-reviewed journal papers
- Learn how to translate scientific findings and potential impacts in layman’s language.
Summer 2018
HCS 8830
Senescence of Plant Organs
Instructor: Joe Scheerens, scheerens.1@osu.edu
Second 8 week session
Class #: 20665 (Columbus) and 20666 (Wooster)
Summer 2017
HCS 7806
Extraction, Separation, Identification, and Quantification of Plant Compounds
appreciate theoretical and practical aspects of chromatography (TLC, GC, HPLC, FPLC) and electrophoresis, as well as spectrophotometric assays designed to measure purity and activity of extracted compounds. They will also understand how tissue, cell, organelle complexity affects extraction of desired compounds and recognize optimal choices to maximize yields and purity of desired compounds. The importance of sampling error and how to minimize it; and the importance of both replication and the use of proper controls (e.g., internal and external standards) will also be emphasized.