Life Sciences Commons^™

Computational Neuroscience, Michelle Greene, Ns/Py 357 Students

Open Educational Resources

In Fall 2019, the Computational Neuroscience class at Bates College collaborated to begin an open textbook. Eight students across three majors collaborated to present the content they were learning to students who were similar to themselves. This project serves both pedagogical and social goals. By writing for fellow students, we leveraged the power of teaching for learning. By bringing together students of diverse academic backgrounds, we leveraged the power of peer instruction. Finally, by writing in the open, students not only brought their best work forward, but are working to contribute to an open knowledge environment that democratizes information. This …

Microwave Solventless Synthesis Of Meso-Tetrakis (Pentafluorophenyl)Poprphyrin (Tppf20) And Tris(Pentafluorophenyl))Corrole [Chemistry], Sunaina Singh

Open Educational Resources

Organic chemistry is a two-semester course (Organic Chemistry I, SCC 251 and Organic Chemistry II, SCC 252) required for majors in Biology. The SCC 251 course has been designated for the Integrative Learning Core Competency as well the Digital Communication Ability. This course emphasizes the synthesis, structure, reactivity, and mechanisms of reaction of organic compounds. Laboratory stresses various organic synthetic and analytic techniques (distillation, extraction, chromatography and spectroscopy).

This lab provided an opportunity for students to go deeper with the chemistry content by correlating to the concepts they learned in General Chemistry courses such as Valence shell electron pair repulsion …

Titration Of A Newtown Creek Environmental Water Sample To Determine The Amount Of Chloride Ions [Chemistry], Kevin Mark

Open Educational Resources

Main Course Learning Objectives:

The General Chemistry 1 (SCC 201) course has multiple course learning objectives, which articulate key introductory chemistry concepts that all STEM students should possess. In particular, the Newtown Creek titration experiment aligns with SCC 201 learning objectives of:

1. Demonstrate an appreciation of the role of chemistry in various aspects of life
2. Perform basic laboratory skills such as the proper execution of titration techniques
3. Describe and explain the fundamental chemistry concept of solution concentration
4. Analyze and represent experimental data in tables and graphs, interpret experimental results and write laboratory reports

In the SCC 201 laboratory, students are …

Human Biology Oer, Bio 1100, Course Outline, Tatiana Voza

Open Educational Resources

This course will include selected biological concepts, including the chemical basis of life, cell structure and division, a broad survey of the major systems of the human body with a special emphasis on human health disease, human evolution and ecology. This course should provide students who do not plan to continue in the sciences or pre-health programs with a working knowledge of life science that will be useful in making informed decisions on health and the environment

Environmental Cost Vs. Health Benefit Of Radioisotope Usage In Medicine, Nicholas Whiting

Open Educational Resources

This module is developed for implementation in a class that discusses the use of radioisotopes in a biomedical setting. The inspiration is a class I teach (Advanced Biomedical Instrumentation), which covers the use of radioisotopes as tracers in biomedical imaging (scintigraphy, SPECT, PET, etc.). The goal of the module is to go further in depth regarding the environmental impact of the use of radioisotopes (from their generation to their disposal—keeping track of any radioactive byproducts), and compare that to the potential for benefits in the quality and/or quantity of a patient’s life (does using the radioisotopes allow patients to live …

Are Humans Natural? Part 3: Nature Relatedness And The American Dream, Nathan Ruhl, Taylor Dobson

Open Educational Resources

This learning module is part of a series of activities designed to encourage students to develop relational values with nature. In this activity, students reflect on their relationship with nature and consider the impact of their plans/goals for the future on the environment and the larger goal of sustainability. Students evaluate their relationship with nature through the Nature Relatedness (NR-6) Test (Nisbet and Zelenski, 2013), compare their NR-6 score to others, consider how their goals (“dreams”) are related to the American Dream, and speculate on the attainability of sustainability given our individually driven goals for the future. This activity challenges …

Are Humans Natural? Part 2: Exploring Human-Nature Relational Values And The Balance Of Nature, Nathan Ruhl

Open Educational Resources

This learning module is part of a series of modules that seeks to help students develop human-nature relational values. Relational values are more readily developed when the methods employed reference species/environments/landscapes/situations that students are familiar with already and may encounter during their everyday lives. In this activity students are asked to consider whether nature is in balance. The idea that nature is in balance extends deep into human history, but modern scientific evidence clearly demonstrates that nature is not in balance. Despite scientific evidence, the perception that nature is stable or in balance persists in human culture. This activity challenges …

Fetal Pig Dissection Manual (Biol 105), Nathalia G. Holtzman, Daniel J. Yakubov

Open Educational Resources

This book is a guide to the basic fetal pig dissection conducted as a part of the Queens College, CUNY Biology Department Bio105 General Biology: Physiology and Cell Biology course. This course is the first half our two-part series for biology majors. The actives are designed to be conducted over a three- 3-hour lab periods which focus on the relationship of form and function of the pig anatomy and physiology. Step by step instructions for the dissection are provided along with some microscopy tasks to look at the histology of key organs.

In addition to the full text of the …

Histology Atlas: Basic Mammalian Tissue Types (Biol 105), Joshua Barnes, Daniel J. Yakubov, Corinna Singleman, Nathalia G. Holtzman

Open Educational Resources

This book is a guide to the basic histology lab conducted as a part of the Queens College, CUNY Biology Department Bio105 General Biology: Physiology and Cell Biology course. This course is the first half our two-part series for biology majors. The actives are designed to be conducted over a single 3-hour lab periods which focus on the relationship of form and function of the cellular and organ level anatomy and physiology. Step by step instructions for each slide set are provided for all the key organs.

In addition to the full text of the book, we also provide a …

Writing For Sciences, Michael Coppola

Open Educational Resources

No abstract provided.

Scavenger Hunt Reflection Lab Report, Angela Padilla

Open Educational Resources

A. Scavenger Hunt Description

❏ This Scavenger Hunt Assignment is designed for the First Year Seminar for Natural Sciences (NSF 101) and the First Year Seminar for Liberal Arts: Math and Science (LMF 101) (STEM majors).

❏ The main objective of this assignment is to familiarize students with their campus and its resources, to encourage students to collaborate with each other, and to be aware that the scientific method is applied to solve any problem, not just scientific issues. It is meant to address the Integrative Learning Core Competency.

❏ Students are given the entire class time (at least two …

Crispr/Cas9 In Yeast: A Multi-Week Laboratory Exercise For Undergraduate Students, Randi J. Ulbricht

Open Educational Resources

Providing undergraduate life-science students with a course-based research experience that utilizes cutting-edge technology, is tractable for students, and is manageable as an instructor is a challenge. Here, I describe a multi-week lesson plan for a laboratory-based course with the goal of editing the genome of budding yeast, Saccharomyces cerevisiae. Students apply knowledge regarding advanced topics such as: CRISPR/Cas9 gene editing, DNA repair, genetics, and cloning. The lesson requires students to master skills such as bioinformatics analysis, restriction enzyme digestion, ligation, basic microbiology skills, polymerase chain reaction, and plasmid purification. Instructors are led through the technical aspects of the protocols, …

Sensory Perception, Adrian Rodriguez-Contreras

Open Educational Resources

Different types of sensory systems with their functional modalities will be presented. The biological bases for how these functions are generated and modified will then be described. As vision is the principal means of perception, we will focus in this course most on visual processing. Scientific data will be integrated into the lectures, such that students develop critical skills in analyzing data and proposing hypotheses.

Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim

Open Educational Resources

This material introduces Linux File System structures and demonstrates how to use commands to communicate with the operating system through a Terminal program. Basic program structures and system() function of Perl are discussed. A brief introduction to gene-sequencing terminology and file formats are given.

Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim

Open Educational Resources

This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided, connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to enter the data folder, which includes gene-sequencing input files and print the first five line of each file remotely. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the VMI can be used to do the exercise.

Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim

Open Educational Resources

This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided and connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to automate the tasks to create VCF files from two different sample genomes belonging to E.coli microorganisms by using the FASTA and FASTQ files in the input folder of the virtual machine. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the …

Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim

Open Educational Resources

This material briefly reintroduces the DNA double Helix structure, explains SNP and INDEL mutations in genes and describes FASTA, FASTQ, BAM and VCF file formats. It also explains the index creation, alignment, sorting, marking duplicates and variant calling steps of a simple preprocessing workflow and how to write a Perl script to automate the execution of these steps on a Virtual Machine Image.

Designing Computational Biology Workflows With Perl - Part 1 & 2, Esma Yildirim

Open Educational Resources

This manual guides the instructor to combine the partial files of the virtual machine image and construct sequencer.ova file. It is accompanied by the partial files of the virtual machine image.

Bioinformatics Ii, Bio 3352, Course Outline, Eugenia G. Giannopoulou

Open Educational Resources

This course is a continuation of Bioinformatics I. Topics include gene expression, microarrays, next- generation sequencing methods, RNA-seq, large genomic projects, protein structure and stability, protein folding, and computational structure prediction of proteins; proteomics; and protein-nucleic acid interactions. The lab component includes R-based statistical data analysis on large datasets, introduction to big data analysis tools, protein visualization software, internet-based tools and high-level programming languages.

Human Anatomy And Physiology I: Course Map With Expected Learning Outcomes, Carlos Liachovitzky

Open Educational Resources

This document contains a list with all the Anatomy and Physiology I expected learning outcomes organized by topics, and grouped into ten units: 1. Introduction to A&P: body plan & organization; 2. Introduction to A&P: homeostasis; 3. The chemical level of organization; 4. Levels of organization: the cellular level of organization; 5. Levels of organization: the tissue level of organization; 6. Support and movement: integumentary system; 7. Support and movement: skeletal system & articulations; 8. Support and movement: muscular system; 9. Regulation, integration, and control: nervous system; 10. Regulation, integration, and control: special senses

Each learning outcome is referred to …

Zero Textbook Cost Syllabus For Env 3009/4900 (Conservation Biology And Sustainable Development), Stephen Gosnell

Open Educational Resources

Conservation biology is an interdisciplinary topic that explores how we can protect and maintain natural areas. Due to the resources we take and impacts we have on natural environments, this field is directly related to restoration ecology (restoring natural areas) and sustainable development/natural resource management. We will explore the basis for these related fields from an ecological, social, legal, and cultural perspective, as all conservation and management projects take place in the larger human landscape. We will consider how we measure biodiversity, why it matters, why is it is threatened, and how we can manage (protect, restore, maintain, use) it …