Current Topics and Methods Courses

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:

1. To better understand mechanisms of abiotic stress tolerance in plants. 
2. To differentiate between plastic responses and adaptations, whether inducible or canalized.
3. 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

• Mon (lecture) 2-3pm; Mon (lab) 3-5pm, video-link to Wooster
• Howlett 139; Gourley 102

HCS 8830

Principles and Applications of Plant Hormone Signal Transduction Mechanisms

HCS 8830

Crop Mythbusters- What Works and What Doesn't

AUTUMN 

Autumn 2020

HCS 7806

Methods in Data Visualization

Instructor: Jessica Cooperstone, cooperstone.1@osu.edu

14 weeks, 2 credit hours

Meeting time: Tuesdays, 1:50-3:40pm; synchronously over Zoom

Class numbers: 35916 (Columbus) and 35917 (Wooster)

Want to gain additional skills in transforming your raw data to publication-quality figures?  The purpose of this methods class is to:

1. Understand basic principles of data visualization and distinguish effective figures from ineffective ones
2. Gain competency in using ggplot2 and other R visualization tools (and if you have no R experience or want to brush up, I will provide you some resources to gain basic competency)
3. Take your own data, data generated by your lab, or publicly available data and turn it into publication quality figures.

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:

1. Nature of this hormone (1 slide).
2. History of this hormone (1 slide).
3. Biosynthesis and metabolism of this hormone (1 to 2 slides).
4. Functions of this hormone (1 to 2 slides). See examples of info via http://pages.wustl.edu/ipgsa/plant-hormones
5. 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.
6. 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 2020

HCS 8830 

Weed Seed Biology

Instructor: Doug Doohan. doohan.1@osu.edu

1 credit

Class numbers: 22394 (Columbus), 22395 (Wooster)

Meeting Times: Class time will be by arrangement but most likely will occur over the lunch hour period.

Locaiton: ZOOM (This will be entirely online)

Enrollment cap: 5

This class will explore contemporary literature dealing with the biology of buried weed seeds and research methods used to explore the same.  The class will meet via Zoom for 4 hours each week during the May Semester and will receive a letter grade.  Students will be expected to contribute to all discussions and lead one or more. Interested students should contact Dr. Doohan

HCS 8830 

Instructor: Joe Scheerens, scheerens.1@osu.edu 

8-week session 2

Class numbers: 20175 (Columbus), 20176 (Wooster)

Topic determined by student consensus

Time/Location: ZOOM (This will be entirely online)

HCS 7806

Fundamentals of Molecular Population Genetics

Instructor: Jonathan Fresnedo, fresnedoramirez.1@osu.edu  

4-week Session 3, Summer 2020, 1 credit

Meeting time: Monday, Wednesday and Friday at 1:50 PM 

Class #: 22166 

55-minute lecture on Monday and Wednesday; 110-minute computer lab on Friday

The aim of this course is to enable graduate students to become familiar with historical conceptual foundations in population genetics and to examine applications of these concepts in the analysis of molecular data. The goal of this course is that graduate students acquire theoretical concepts and insights to interpret molecular population genetic analyses for subsequent, independent pursuits of literature reviews or organized study groups to address advanced topics related to population genetics. 

The evaluation for this course will be based on weekly quizzes in Carmen.

The structure of the course is as follows:

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

HCS 8830

HCS 8830