AET 703 Technology Management Analytics

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Sheet1

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Annotated bibliography

Name

Professor

Institution

Course

Date

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Ying, W. (2018). Research on the Adaptability of Building Materials Application in Exterior

Exterior Design of Buildings. IOP Conference Series: Earth and Environmental

Science, 189, 032009. https://doi.org/10.1088/1755-1315/189/3/032009

The article explores building outdoor structures; the research of Wu Ying focuses on

the flexibility of building materials. Advances in building technology have risen in line with

the growing need for better-quality building materials. To maintain the benefits of the grand

design of building materials and ensure that their design level is progressively enhanced to

enhance the exterior design of buildings, a focus on the adaptability research of building

materials application is needed. Building materials can be used in various ways; they can

enhance the appearance of modern building engineering, increase project value, and increase

building field production efficiency by examining their adaptability to the external design

shape of a building (Ying, 2018).

The relevance of the resource explains how building materials are adapted to creating

an exterior of a building and help increase the production efficiency of the building field.

Perez, G., & Perini, K. (2018). Nature-Based Strategies for Urban and Building

Sustainability. In Google Books. Butterworth-Heinemann. https://books.google.co.ke/

books?

id=_wIxDwAAQBAJ&dq=nature+and+sustainability+of+a+building&hl=en&sa=X&

ved=2ahUKEwjrhdKOmZ_2AhVPUxoKHeBJDsUQ6AF6BAgKEAI

The article by Perez and Perini analyses the current state of the art on nature-based

urban and building sustainability strategies, discussed in detail. In the introduction, the

editors cover essential principles of natural components in the built environment and a

strategy for their use in buildings and cities. Part One discusses urban ecosystems and

3

ecosystem services. In contrast, Part Two focuses on tactics and technology, such as vertical

greening systems, green roofs, and green streets, to improve the urban environment. Aspects

such as improved energy efficiency, air quality, acoustics, water management, and

biodiversity are addressed in Part Three, including data on the project’s quantitative

outcomes. Describes the many ways to incorporate nature into the built world. Systems and

approaches for incorporating nature into buildings are presented in this article—the most up-

to-date information on operations and ecosystem services research. This collection includes

new and established designs and those currently in the testing phase (Perez & Perini, 2018).

The article is essential because It enables a great understanding of the strategies used

by Leoh Ming to integrate the city environment with the building. However, the book has no

reviews yet; the authors are researchers with Ph.D. degrees and have experience in their field

of work. This makes the source to be reliable and trustworthy.

Puspitasari, A. W., & Kwon, J. (2020). A reliable method for visibility analysis of tall

buildings and skyline: a case study of tall buildings cluster in Jakarta. Journal of

Asian Architecture and Building Engineering, 1–12. https://doi.org/

10.1080/13467581.2020.1787839

High-rise and skyline visibility analysis is the subject of this essay. Decisions

concerning the skylines of modern cities, dominated by skyscrapers, must take visibility into

account. Using a targeted isovist is the cornerstone of the visibility approach, which refers to

the visible portion of a tall structure’s target area. Analysis of tall tower clusters visible from

adjacent streets and the effect they have on the city’s skyline is presented in this article, which

uses Jakarta as an opportunity to illustrate how this approach may be applied to other cities.

To replicate the modeling techniques in the background, Grasshopper was utilized to create

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the algorithm for visualizing the content. To illustrate the results, a color section is used to

depict the fraction of viewable viewpoints and the visible space of a structure’s front, both of

which are essential metrics. According to the results, building height combinations, structure

placement, building-to-street relationships, and perspective distances all had a substantial

influence on the rate of visibility. Because of how well they can be seen, tall building cluster

visibility affects its skyline. The techniques provided here for analyzing visibility are

essential for the design and construction of tall buildings in a distributed organization and, as

a result, for predicting how future cities’ skylines will look(Puspitasari & Kwon, 2020).

The significance of the article will enable me to understand the position of

structures, the relationship between the buildings and the street, the distances between

different perspectives what significant impact they play on the rate of visibility.

Abdelhameed, W., & Saputra, W. (2020). Integration of building service systems in

architectural design. Journal of Information Technology in Construction, 25, 109–

122. https://doi.org/10.36680/j.itcon.2020.007

It examines the importance of structure service systems (BSS) and how they’re being

considered at the earliest phases of architectural design. If these technologies are included in

the structure’s design rather than after being built, it will save money and time. The late

inclusion of BSS may have a detrimental impact on both the structure’s exterior and inside.

Since it may enhance design outcomes while also identifying and eliminating service system

incompatibilities and conflicts. BSS integration is becoming more common in the

construction sector, notably plumbing systems and the design itself, and between the design

and the design, all benefit from 3D digital modeling. 3D digital modeling is critical in

spotting possible conflicts. All service systems are coordinated using various methods studied

in the literature. Additional data from the construction industry is also being collected and

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evaluated to offer a more objective perspective. BSS are integrated into the architectural

design throughout the conceptual phases of the design process, using a variety of regional

construction projects and research on the construction industry as examples(Abdelhameed &

Saputra, 2020).

The article is relevant since it explores how to improve design results while also

detecting and avoiding service system incompatibilities and conflicts.

Bradecki, T., & Uherek-Bradecka, B. (2017). Work Models in the Design Process for House

Interior and Exterior: Physical or Virtual? IOP Conference Series: Materials Science

and Engineering, 245, 052033. https://doi.org/10.1088/1757-899x/245/5/052033

The results of a study into several kinds of single-family and multifamily housing

models are presented in this article. The outside layout and internal functional arrangement

heavily influence the design outcome. Models are essential tools for architects to use while

showcasing their work and educating the public about their concepts. Even though 3D

models may depict anything, specific individuals still cannot grasp the concept of the planned

place. The researchers’ goal is to find a way to stimulate both the inside and outside of a

vehicle in a single model. In the article, a variety of home models are shown. We used a

combination of actual models, 3D models, and hand drawings to create each of the case

studies we’ve done.

The resource’s importance with the models was to get a clear picture of how planned

future homes would feel in terms of openness. According to the study’s findings, synthetic

models may aid in the design process.

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The URBAN model research group, which includes academic researchers and

architects, researches relevance. The authors gained a plethora of architectural expertise via

theoretical models, building projects, and construction site monitoring. The following

information may be of interest to builders, designers, interior designers, and academics in

architecture. (Bradecki & Uherek-Bradecka, 2017).

7

Reference

Ying, W. (2018). Research on the Adaptability of Building Materials Application in Exterior

Exterior Design of Buildings. IOP Conference Series: Earth and Environmental

Science, 189, 032009. https://doi.org/10.1088/1755-1315/189/3/032009

Perez, G., & Perini, K. (2018). Nature-Based Strategies for Urban and Building

Sustainability. In Google Books. Butterworth-Heinemann. https://books.google.co.ke/

books?

id=_wIxDwAAQBAJ&dq=nature+and+sustainability+of+a+building&hl=en&sa=X&

ved=2ahUKEwjrhdKOmZ_2AhVPUxoKHeBJDsUQ6AF6BAgKEAI

Puspitasari, A. W., & Kwon, J. (2020). A reliable method for visibility analysis of tall

buildings and skyline: a case study of tall buildings cluster in Jakarta. Journal of

Asian Architecture and Building Engineering, 1–12. https://doi.org/

10.1080/13467581.2020.1787839

Abdelhameed, W., & Saputra, W. (2020). Integration of building service systems in

architectural design. Journal of Information Technology in Construction, 25, 109–

122. https://doi.org/10.36680/j.itcon.2020.007

Bradecki, T., & Uherek-Bradecka, B. (2017). Work Models in the Design Process for House

Interior and Exterior: Physical or Virtual? IOP Conference Series: Materials Science

and Engineering, 245, 052033. https://doi.org/10.1088/1757-899x/245/5/052033

HSDD 5300 – Legal & Ethical Issues in Disabilities
Se me ste r and Ye ar: Winter 2022

I. Course Information
Se me ste r and Ye ar: Winter 2022
Course Start and End Date s: 01/03/2022 – 05/01/2022
Course CRN and Se ction: 30115 – L01
B uilding and Room: Online Venue – CANVAS

II. Instructor Information
Profe ssor: Marilyn S Anglade
Email: manglade@nova.edu

If the instructor cannot be reached, please contact the Department offering this course.

III. Class Schedule and Location
Day Date Time Location Building/Room

01/03/2022 – 05/01/2022 Programs On-line Online Venue-CANVAS

IV. Course Description
This course discusses current laws related to disabilities, such as ADA and IDEA, as well as
contemporary issues affecting the lives of individuals with disabilities and the daily responsibilities of
disability professionals. This course further examines the application of ethical principles to matters
associated with genetics, treatment decisions, and competency determination. P rerequisite: HSDD 5000

V. Course Objectives / Learning Outcomes
1) Discuss the importance and impact of disability law such as ADA and IDEA.
2) Demonstrate an understanding of the most common ethical issues affecting individuals with disabilities
and disability professionals.
3) Demonstrate an understanding of the application of ethical principles to the resolution of common
dilemmas in the disability field.

VI. Materials and Resources
B ook Url: NSU Book Store
Course Re quire d Te xts and M ate rials:
We hme ye r, M . L., B rown, I., Pe rcy, M ., Shogre n, K. A. & Fung, W. L. A. (2017). A
comprehensive guide to intellectual and developmental disabilities. B rooke s. ISB N:978-1-59857-
602-3

American P sychological Association. (2019). Publication Manual of the American Psychological
Association (7th ed.). Author. ISB N: 978-1-4338-3217-8

Course Supple me ntal M ate rials:
Ouellette, A. (2013). Bioethics and disability: Toward a disability-conscious bioethics. Cambridge
University P ress.

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U.S. Department of Justice Civil Rights Division Disability Rights Section. (n.d.). A Guide to Disability
Rights Laws. https://www.ada.gov/cguide.htm

He lpful We bsite s:
Americans with Disabilities Act (ADA). (n.d.). Information and technical assistance on the
Americans with disabilities education act. https://www.ada.gov/2010_regs.htm

The National Alliance for Direct Support P rofessionals
(2020). Frontline initiative. https://nadsp.org/frontline-initiative/
US Department of Education. (n.d.). Office of Special Education and Rehabilitative Services.
http://www2.ed.gov/about/offices/list/osers/osep/index.html
US Department of Labor. (2020). Office of Disability Employment Policy.
https://www.dol.gov/agencies/odep

VII. Course Schedule and Topic Outline
Class schedule subject to modification, but not without prior notification.
Course Sche dule :

**Class schedule subject to modification, but not without prior notification.**
We e k Topic

Week
1 1/3-
1/9

Ethics of Decision Making and Consent in P eople with Intellectual and Developmental Disabilities

Week
2
1/10-
1/16

Changing P erspectives on Intellectual and Developmental Disabilities

Week
3
1/17-
1/23

Trends and Issues in Intellectual and Developmental Disabilities

Week
4
1/24-
1/30

Responding to Cultural and Linguistic Differences Among P eople with Intellectual Disability

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Week
5
1/31-
2/6

Maltreatment of Children with Developmental Disabilities

Week
6
2/7-
2/13

Sexuality and P eople Who Have Intellectual and Developmental Disabilities

Week
7
2/14-
2/20

Historical Overview of Intellectual and Developmental Disabilities

Week
8
2/21-
2/27

What Is Meant by the Terms Intellectual Disability and Developmental Disabilities?

Week
9
2/28-
3/6

Spring Break

Week
10
3/7-
3/13

Advocacy and Legal Considerations to Ensure Civil Rights

Week
11
3/14-
3/20

Self-Advocacy

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Week
12
3/21-
3/27

Nutritional Considerations for Children with Intellectual and Developmental Disabilities

Week
13
3/28-
4/3

Making Services More Effective Through Research and Evaluation

Week
14
4/4-
4/10

P eople with Intellectual and Developmental Disabilities and Mental Health Needs

Week
15
4/11-
4/17

Future Trends and Advances in Intellectual and Developmental Disabilities

Week
16
4/18-
4/24

Introduction to Early Development: A Multidisciplinary P erspective

Week
17
4/25-
5/1

Introduction to Genetics, Genomics, Epigenetics, and Intellectual and
Developmental Disabilities

VIII. Assignments
Assignme nt # 1: Disability Encounte r Re action Pape r (Due we e k 4)
Students will be asked to write a short reflection paper (3 pages) describing one of
the following encounters with disability:
• Interview a person with a disability and provide transcript
• Read a first-person account of a person with a disability

The reflection paper will focus on basic information about the type of disability as well as the individual’s
experience(s) of and attitude(s) towards the disability. Be sure to use literature to support your statements
(at least 3 citations from disability-related journals). When citing the literature, please remember to follow

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APA style.

P age 1: Background and description of the disability
P age 2: Description of your encounter (i.e. describe the interview, summarize the articles read, summarize
biographical description)
P age 3: Reflect on the individuals experiences and provide personal reactions/reflections to your
experiences learning from an individual with a disability.

Assignme nt # 2: Ethical Issue s and Challe nge s Re action Pape r (Due we e k 11)
Students will be expected to discuss the common issues and challenges when working with individuals with
disabilities, including methods of overcoming these challenges while considering ethical and legal aspects
along the way. In addition, talk about how specific laws, such as ADA, IDEA, etc… play a role in
addressing the challenges and issues encountered. Be sure to use literature to support your statements (at
least 5 citations from disability-related journals). Your paper should be between 4 to 5 pages. When citing
the literature, please remember to follow APA style.

P age 1: Identify common issues and challenges when working with individuals with disabilities
P age 2: Discuss ethical and legal aspects of the issues/challenges you presented
P age 3-4: Discuss laws (ADA, IDEA, etc) and how they can specifically play into supporting or
hindering individuals encountering the common issues/challenges you identified.
P age 5: Discuss your personal reflections, thoughts, ideas

Assignme nt # 3: Program Re se arch Pape r (Due we e k 13)
Students are expected to produce a 8-10 page paper with at least 10 citations from disability-related
journals. When citing the literature, follow APA style. For this assignment, students are to DESIGN a
service program for individuals with a specific disability including the following components: administrative
considerations, ethical and legal considerations, managing staff and workplace conflict, and utilizing well
researched and effective techniques with the population chosen.

P age 1: Identify and describe a disability
P age 2-3: Describe a program need for individuals with this disability (cite current research surrounding
this need, what programming currently exists, why additional programming is needed.)
P age 4-6: Discuss your program design in detail using research-based techniques. P ages 7-8 Include
additional sections to discuss any legal/ethical considerations that may emerge with the program you are
implementing.
P ages 9-10: Include personal reflections/opinions, ideas for future research.

Assignme nt # 4: Program Re se arch Pre se ntation (Due we e k 14)
Students are expected to create a power point presentation of 10-15 slides discussing their assignment #3
papers. These presentations will be shared during class and posted.

Discussion Posts: (Due throughout the se me ste r)
Throughout this course, you will be prompted to respond to a discussion question. Discussion post
assignments are due as indicated on the course schedule. P rior to completing the discussion post, you
should read all assigned material for the week so as to incorporate what you’ve learned (and any additional
research you’ve done) into your response. Your discussion posts should not solely consist of your opinions
– all opinions/conclusions should be supported by research and/or the text demonstrating your
understanding of the assigned materials. For each discussion post, you are required to respond to one
classmate’s post. Both your initial post as well as your response post must be submitted by the Sunday of
that week by 11:59 p.m., EST.

Chat participation:
There will be four (4) live chat sessions, held via Zoom, throughout the semester. Students who are unable
to attend the live session should submit a one (1) paragraph synopsis of the discussion held in order to

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obtain points for attendance. See “course policies” below for further information.

IX. Grading Criteria
Your final grade is determined by your performance on a number of different tasks:
Grade Quality P oints P ercentage P oints

A 4.00 90 – 100

B 3.00 80 – 89

C 2.00 70 – 79

F 0.00 Below 70

NP R 0.00 –

P 0.00 –

Additional Grade s: I (Incomplete), W (Withdrawn), AU (Audit), NPR (No P rogress), and TR
(Transfer). The grade of PR (P rogress) may be used for programs with a thesis or dissertation in which
the student continues to demonstrate progress towards requirement completion. P rograms with clinical
rotations, internships, or externships in which grades may not be available within the university’s approved
grading period may use the IP (In P rogress) grade.

Final Course Grade :
GRADING CRITERIA: Your final grade is determined by your performance on the following grade
categories and scale
GRADE CATEGO RIES WEIGH T

Assignment #1: Disability Encounter Reaction P aper 15%

Assignment #2: Ethical Issues & Challenges Reaction P aper 15%

Assignment #3: P rogram Research P aper 15%

Assignment #4: P rogram Research P resentation 25%

Discussion P osts (x7) 20%

P articipation in Live Chats (x4) 10%

TOTAL: 100%

X. Course Policies
Ge ne ral Policy:
This course consists of readings, live classes, and discussions. While you are not required to attend live
sessions, you are strongly encouraged to do so. Students who do not attend a live session should listen to a
recording of that week’s discussion which will be posted on the Canvas site within 48 hours of the live
session. To obtain points for the session, students are required to submit a 1 paragraph synopsis of the
discussion held during that live session. Students are charged with the knowledge and information
disseminated during the live sessions. Therefore, while attendance is not mandatory, reviewing the
recording is suggested such that students are kept abreast of course information. While previous
knowledge and/or experience are not required for this course, it is the responsibility of the student to
contact the instructor to clarify any issues regarding the concepts being studied each week.

Specifically, this course is taught in eight week-long sessions. The materials are presented in eight weekly

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modules. Each week, the Module will open on Monday at 12:01 a.m. EST and will close the following
Sunday. All assignments for a given week will be due on Sunday at 11:59 p.m. EST. In addition to the module
material, we will have 4 live chat sessions, as noted above in the course schedule. Each week, the student is
expected to complete the assigned readings as well as either a research/reaction paper or a discussion post and
response.

If a student anticipates being unable to complete an assignment by the listed deadline, he/she may contact
the instructor for a possible extension. Stude nts should not assume the y will be grante d an
e xte nsion but must contact the instructor for further information.

Both the subjects covered and the required readings may necessitate modification during the semester.
The instructor will make every effort to advise students of any changes. However, it is the responsibility
of the student to check the course site often for adjustments made to the syllabus or for any other
announcements.

The Internet is an extension of the classroom. As such, the decorum and professionalism expected of you
in class extends to the Website and all postings made regarding the course or its content. I expect that you
will extend the same courtesy to your fellow students on the list as you do in class. Feel free to disagree
with the ideas expressed but work to keep the discussions polite and focused on the ideas.

XI. University Policies
P lease consult the FCE catalog for information on college and department policies and the NSU Student
Handbook for information on NSU policies: https://education.nova.edu/students/current-
students/studentcataloghandbook.html

NSU Class Recording P olicy:
Class content throughout this course may be recorded in accordance with the NSU Class Recording
P olicy. If class content is recorded, these recordings will be made available to students registered for this
course as a supplement to the classroom experience. Recordings will be made available to all students who
were registered to attend the live offering of the class, regardless of a student’s section or discipline, or
whether the student is participating in the course online. If recordings are intended to be accessible to
students or third parties who were not registered for the live offering of the class, students’ personally
identifiable information will be removed or redacted from the recording, unless (1) their written consent to
such disclosure was previously provided, or (2) the disclosure is permissible in accordance with the Family
Educational Rights and P rivacy Act (“FERPA”).
Students are prohibited from recording audio or video, or taking photographs in classrooms (including online
classes) without prior permission from the instructor or pursuant to an approved disability accommodation,
and from reproducing, sharing, or disseminating classroom recordings to individuals outside of this course.
Students found engaging in such conduct will be in breach of the Student Code of Conduct and subject to
disciplinary action.

XII. Bibliography
McAfee, J. K., Cockram, J., & Wolfe, P. S. (2001). P olice reactions to crimes involving people with
mental retardation: A cross-cultural experimental study. Education and Training in Mental Retardation
and Developmental Disabilities, 36, 160-171.
Morris, C. D., Niederbuhl, J. M., & Mahr, J. M. (1993). Determining the capability of individuals with
mental retardation to give informed consent. American Journal of Mental Retardation, 98, 263-272.
Niederbuhl, J. M., & Morris, C. D. (1993). Sexual knowledge and the capability of persons with dual
diagnoses to consent to sexual contact. Sexuality & Disability, 11, 295-307.
P arker, T., & Abramson, P. R. (1995). The law hath not been dead: protecting adults with mental
retardation from sexual abuse and violation of their sexual freedom. Mental Retardation, 33, 257-263.
P etersilia, J. (1997). Unequal justice? Offenders with mental retardation in prison. Corrections

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Management Quarterly, 1(4), 36-43.
P etersilia, J. (2000). Doing justice? The criminal justice system and offenders with developmental
disabilities. California P olicy Research Center, University of California: Los Angeles, CA.
Stavis, P. F. (1991). Harmonizing the right to sexual expression and the right to protection from harm for
persons with mental disability. Sexuality and Disability, 9, (2), 131-141.

XIII. Appendix/Appendices
P lease refer to the grading rubrics below for specific scoring:

Rubric for Classroom Participation
Criteria 0 points 1 point 2-3 points

Actively contributes to
classroom discussions

P rofessor has no
ability to connect
student’s name,
voice, and ideas.
Student “multi-
tasks” or distracts
others in class.

Student follows
classroom discussion
and offers thoughts
during some classes.

Student initiates
discussions or actively
contributes to
discussions in a
variety of ways,
including those below.

Displays awareness of
class readings

Contributions
display lack of
awareness of the
readings.

Contributions display
tangential or vague
awareness of
readings.

Contributions
connected to readings.
Student able to
reference ideas from
the readings.

Generates
questions/challenges

Student passively
accepts, passively
rejects, or gives up
on ideas from
readings.

Student participates in
discussions of
questions related to
readings, or testing of
ideas.

Student initiates
questions arising from
the reading or
challenges ideas in
response to other,
contrasting ideas.

P resents areas of
confusion/“miss-
understandings”

Student presumes
that confusion is a
statement about
their own
inadequacies, or
the difficulty of the
content, and
remains silent.

Student participates in
discussions about
areas of confusion or
“miss-
understandings.”

Student raises areas
of confusion and
collaborates with
seminar members to
think through
confusions and “miss-
understandings.”

Rubric for Discussion Postings

Criteria 0-1 point 2 points 3-4 points

Sufficient number of
contributions

Less than six
contributions, and/or
contributions only
added at the last
minute, and/or few
visits to site

Six contributions
and/or site visited
once per week or
less.

More than Six
contributions and site
visited once per
week or more.

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Contributions related
to readings/
discussions

Contributions
unrelated to course
content

Contributions
related to others’
comments about
the course material,
without adding new
responses related
to course material

Contributions are
clearly that
—contributions that
draw from (with
citations) course
readings/discussions.

Engagement of
contributions

Contributions only
congratulatory,
critical, and/or of the
“thanks-that-was-
great” variety

Contributions relate
to and expand upon
the contributions of
others.

Contributions initiate
new threads and/or
introduce new ideas
to discussion.

Rubric for Re action Pape rs Assignme nts 1 and 2

0-2 points 3-4 points 5-7 points Comments

P resents own
ideas, thoughts,
questions around
personal reflection,
the course, or
other relevant
matters stemming
from participation
in the course

P aper is based
solely on course
content, e.g. a
summary of one
of the chapters
or articles.

Some, thin
discussion of
personal
reflections
based on the
course content

P aper reflects
personal
consideration of
personal reflection,
the course or other
relevant matters
stemming from
participation in the
course.

Relates own
thoughts to
specific course
content,
particularly
readings, and other
empirically
validated and
supportive
literature

Reflections are
entirely personal
without
evidence of
engagement
with course
readings or
experience.

P ersonal
reflections
related to
course
materials and
research
literature, but
these are not
specifically
cited.

P ersonal reflections
are founded in
course materials,
particularly based
on specific
reference to course
readings and
research literature.
Reference to class
discussions may be
included.

Adheres to APA
format; well-
written.

Multiple errors
in APA format;
errors from
previous papers
not corrected in
subsequent
papers. Writing
poorly edited;
awkward
construction
and/or poor flow
of ideas.

Some APA
errors. Writing
shows
evidence of
self-editing
with some
construction
and/or flow
problems.

Accurate use of
APA format with
minimal errors.
Evidence that errors
from previous
papers are
corrected in later
papers. Coherent
development of the
ideas using well-
formed sentences
and flowing
paragraphs.

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Rubric for Program Re se arch Pape r Assignme nts 3

0-2 points 3-4 points 5-7 points Comments

P resents ideas,
thoughts, and
questions in a
manner that
addresses the
research question
chosen and
relates
information to
course content.

P aper does not
fully answer the
research
question
chosen.

Some
components of
the question
chosen are
addressed and
integration of
student’s
ideas,
thoughts, and
questions with
course content
is noted.

P aper reflects full
integration of
personal ideas,
thoughts, and
questions with
course content and
all components of
the question chosen
are answered
thoroughly.

Information
presented
provides evidence
of knowledge and
skills gained
through research,
as well as
application of
these skills.

Responses to
the question
chosen are
entirely
personal
without
evidence of
engagement
with course
readings,
experience, or
supportive
literature.

P ersonal
responses to
the question
chosen are
related to
course
materials and
supportive
literature but
these are not
specifically
cited.

P ersonal responses
to the question
chosen are founded
in course materials,
particularly based
on specific
reference to course
readings and
research literature.
In addition, there is
evidence of the
application of
knowledge and
skills learned.

Adheres to APA
format; well-
written.

Multiple errors
in APA format;
errors from
previous papers
not corrected in
subsequent
papers. Writing
poorly edited;
awkward
construction
and/or poor
flow of ideas.

Some APA
errors. Writing
shows
evidence of
self-editing
with some
construction
and/or flow
problems.

Accurate use of
APA format with
minimal errors.
Evidence that
errors from
previous papers are
corrected in later
papers. Coherent
development of the
ideas using well-
formed sentences
and flowing
paragraphs.

Rubric for Program Re se arch Pre se ntation Assignme nt 4

0-2 points 3-4 points 5-7 points Comments

Generated: 3/1/2022 Page 10 of 14

P resents ideas,
thoughts, and
questions in a
manner that
addresses the
research question
chosen and relates
information to
course content.

P resentation
does not fully
answer the
research
question chosen.

Some
components of
the question
chosen are
addressed and
integration of
student’s ideas,
thoughts, and
questions with
course content
is noted.

P resentation
reflects full
integration of
personal ideas,
thoughts, and
questions with
course content and
all components of
the question chosen
are answered
thoroughly.

Student
disseminates
information and
research findings
clearly and
provides their
personal thoughts,
feelings, or ideas
that support or
contradict these
findings.

P resentation
does not provide
information
addresses the
question chosen
nor does it
provide the
audience with
research data
and conclusions.

P resentation
answers the
components of
the question
and presents
some research
data and
conclusions
with no
elaboration or
personal views
mentioned.

P resentation fully
answers the
research question
chosen and provides
detailed research
data and
conclusions. In
addition, the student
provides his/her
personal views that
either support or
contradict the
research findings.

P resentation
generates active
participation from
the audience, as
well as questions
for discussion.

P resentation
generates no
interest from the
audience or any
questions for
discussion.

P resentation
generates
some interest
from the
audience in the
form of active
participation or
some short
questions that
do not lead to
discussion.

P resentation poses
questions to the
audience, engages
them in activity, and
generates many
questions for
discussion.

Stude nts comple ting H SDD 5300 will be able to me e t the following program obje ctive s by the
following asse ssme nt me asure me nts and me thods:
Course : Le gal and Ethical Issue s in Disability

Le arning Outcome s/Obje ctive s
and
Program Obje ctive s

Dire ct Asse ssme nt Asse ssme nt M e thod

Generated: 3/1/2022 Page 11 of 14

Learning Outcome 1:
Discuss the importance and impact of
disability law such as ADA and
IDEA.
P rogram Learning Objectives:
P LO 1: Knowledge of Leadership
P LO 2: Knowledge of Developmental
Disabilities and Challenges
P LO 3: Understanding impact of
systems
P LO 4: Apply ethical and legal
principles
P LO 6: Demonstrate research,
analytic, and writing skills

Discussion P osts,
Ethical Issues and
Challenges Reaction
P aper

A 20-point criterion-based rubric is
used to assess students’ ability to
review literature and discuss how
specific laws play a role in addressing
challenges when working with
individuals with disabilities.

Learning Outcome 2:
Demonstrate an understanding of the
most common ethical issues affecting
individuals with disabilities and
disability professionals.
P rogram Learning Objectives:
P LO 1: Knowledge of Leadership
P LO 2: Knowledge of Developmental
Disabilities and Challenges
P LO 3: Understanding impact of
systems
P LO 4: Apply ethical and legal
principles
P LO 5: Apply knowledge of strategic
planning and administration to provide
services
P LO 6: Demonstrate research,
analytic, and writing skills

Discussion P osts,
Disability Encounter
P aper,
Ethical Issues and
Challenges Reaction
P aper,

A 20-point criterion-based rubric is
used to assess students’ ability to
reflect on an individual with a specific
disability in interviewing and
discussing that individual’s
experiences, attitudes, and challenges
with regard to their disability.
A 20-point criterion-based rubric is
used to assess students’ ability to
review literature and discuss how
specific laws play a role in addressing
challenges when working with
individuals with disabilities.

Learning Outcome 3:
Demonstrate an understanding of the
application of ethical principles to the
resolution of common dilemmas in the
disability field.
P rogram Learning Objectives:
P LO 1: Knowledge of Leadership
P LO 2: Knowledge of Developmental
Disabilities and Challenges
P LO 3: Understanding impact of
systems
P LO 4: Apply ethical and legal
principles
P LO 5: Apply knowledge of strategic
planning and administration to provide
services
P LO 6: Demonstrate research,
analytic, and writing skills

Discussion P osts,
Ethical Issues and
Challenges Reaction
P aper,
P rogram Research
P aper,
P rogram Research
P resentation

A 20-point criterion-based rubric is
used to assess students’ ability to
review literature and discuss how
specific laws play a role in addressing
challenges when working with
individuals with disabilities.
A 20-point criterion-based rubric is
used to assess student’s ability to do
an extensive review of literature in
designing a service program for
individuals with a specific disability.
A 20-point criterion-based rubric is
used to assess student’s ability to
present information retrieved in
research in designing a service
program for individuals with a
specific disability.

Generated: 3/1/2022 Page 12 of 14

Learning Outcome 4:
Recognize the function of his or her
professional code of ethics when
working with individuals with
disabilities.
P rogram Learning Objectives:
P LO 1: Knowledge of Leadership
P LO 2: Knowledge of Developmental
Disabilities and Challenges
P LO 3: Understanding impact of
systems
P LO 4: Apply ethical and legal
principles
P LO 5: Apply knowledge of strategic
planning and administration to provide
services
P LO 6: Demonstrate research,
analytic, and writing skills

Discussion P osts,
P rogram Research
P aper,
P rogram Research
P resentation

A 20-point criterion-based rubric is
used to assess student’s ability to do
an extensive review of literature in
designing a service program for
individuals with a specific disability.
A 20-point criterion-based rubric is
used to assess student’s ability to
present information retrieved in
research in designing a service
program for individuals with a
specific disability.

Learning Outcome 5:
Analyze and apply the appropriate
legal concepts of privacy,
confidentiality, and informed consent
when working with individuals with
disabilities, understanding the unique
factors that affect these concepts with
this population.
P rogram Learning Objectives:
P LO 1: Knowledge of Leadershi

1

Dallas City Hall

Name

Professor

Institution

Course

Date

2

One of the buildings that I chose from Leoh Ming’s architect works is the Dallas City

building located in Dallas, USA. I have chosen the building due to its unique structure and

intention to serve as the administrative center for Dallas’ municipal administration. However,

the structure slopes at a 34-degree inclination, each of the building’s seven above-grade levels

are 9.5-feet wider from the one below it. This sloping façade interacts only with buildings on

either side facing downtown and offers shelter from the elements and the Texas sun. Dallas

City Hall has an extensive façade, concrete structures, and adaptability of construction

materials which are well designed according to the articles the paper presents.

Although the foundation and basement levels are far more extensive than the visible

footprint of the building, they are hidden behind the sloping façade and extend well beyond

it. Two hundred thirty feet in width, the cantilevered roof spans 200 feet (61 meters), the

ground level is 126 feet in width, and the basement is 230 feet. According to the article by

Dallas City Hall, the building façade is inseparable from the park in front of it(Dallas City

Hall, n.d.). Three cylindrical pillars that seem to prop up the structure were constructed due

to the Mayor’s reaction to the apparent upper of the building’s form. In addition to providing

cosmetic support, these pillars do not carry the structure’s weight. The design and

construction of the structure and the Park Plaza and the garage came to more than $70 million

in total.

When designing City Hall, Pei employed cast-in-place concrete structures for the

interior and outside of the building and the building and park itself. Each story is

approximately nine feet larger than that below it, with the building tilting outward at a 34-

degree angle. The symbolic logic and functional logic are both present in the 560-foot-long

from. The building has utilized the following principles in the construction: attraction and

3

engagement, visibility, nature and sustainability, public transportation as well as integration

(Sustainable Construction: Methods and Benefits, 2020). A concrete frame in a building

project consists of columns as well as a mix of technologies that form the structural skeleton

of a structure. This grid of columns and beams is often erected on a concrete slab and serves

to hold the structure’s floors, walls, and cladding, among other things.

Wu Ying’s study focuses on the adaptability of building materials in the construction

of outdoor buildings. To enhance the building’s exterior, adaptation research in the usage of

construction materials must be prioritized. This Research examines building materials’

flexibility in external design form to increase current building engineering look, project

value, and building field production efficiency(Ying, 2018). Compared to other articles, this

article will help me understand more about the Dallas City building. The peer-review

approach is used to maintain academic study quality by having an author’s academic

publication, study, or ideas reviewed by professionals in the same field.

The main argument of Perez and Perini is nature-Based Approaches to Urban and

Residential Sustainability. They discuss the basic principles of natural components in

building design and the tactics required to incorporate them into buildings and towns. The

three parts explore the quantifiable advantages, outcomes, concerns, and challenges of

integrating nature into our constructed environment (Perez & Perini, 2018). In comparison

with other articles, this article will help me understand the strategies used by Leoh Ming to

integrate the city environment with the building. However, the book has no reviews yet; the

authors are researchers with Ph.D. degrees and have experience in their field of work. This

makes the source to be reliable and trustworthy.

4

The main argument of (Puspitasari & Kwon, 2020) analyses the skyline and tall

buildings’ visibility using a dependable approach. According to the Research, towering

building clusters may be studied by looking at all unimpeded views from adjacent streets and

their effect on the skyline using Jakarta as an example. In comparison with other articles, the

article will enable me to understand the visibility of Dallas City Hall and the methods used by

Leoh Ming to ensure the visibility of the building. The article is a peer-reviewed article that

researchers have checked and ensured the quality.

The article’s main argument by (Abdelhameed & Saputra, 2020) describes how the

architectural design incorporates building services. Specifically, the study examines the

relevance of building service systems (BSS) and how they should be considered throughout

the early architectural design stages. These systems should be included in the building from

the early design stages to save money and avoid costly and time-consuming adjustments. In

comparison with other articles, the article explains how rooms are integrated to form one

building. The article will help me in understanding how Leoh Ming was integrated into one

building. The study has certainly been peer-reviewed to retain academic scientific quality. It

puts an author’s scholarly piece or ideas to evaluation by specialists in the same area. 


5

References

Abdelhameed, W., & Saputra, W. (2020). Integration of building service systems in

architectural design. Journal of Information Technology in Construction, 25, 109–

122. https://doi.org/10.36680/j.itcon.2020.007

Perez, G., & Perini, K. (2018). Nature-Based Strategies for Urban and Building

Sustainability. In Google Books. Butterworth-Heinemann. https://books.google.co.ke/

books?

id=_wIxDwAAQBAJ&dq=nature+and+sustainability+of+a+building&hl=en&sa=X&

ved=2ahUKEwjrhdKOmZ_2AhVPUxoKHeBJDsUQ6AF6BAgKEAI

Puspitasari, A. W., & Kwon, J. (2020). A reliable method for visibility analysis of tall

buildings and skyline: a case study of tall buildings cluster in Jakarta. Journal of

Asian Architecture and Building Engineering, 1–12. https://doi.org/

10.1080/13467581.2020.1787839

Ying, W. (2018). Research on the Adaptability of Building Materials Application in Exterior

Exterior Design of Buildings. IOP Conference Series: Earth and Environmental

Science, 189, 032009. https://doi.org/10.1088/1755-1315/189/3/032009

Dallas City Hall. (n.d.). Www.pcf-P.com. Retrieved March 3, 2022, from https://www.pcf-

p.com/projects/dallas-city-hall/

Sustainable Construction: Methods and Benefits | BigRentz. (2020, February 4).

Www.bigrentz.com. https://www.bigrentz.com/blog/sustainable-construction

MKT 345 Milestone Two Guidelines and Rubric
Consumer Buying Process

Overview: For this milestone, due in Module Four, you will prepare a PowerPoint presentation summarizing the consumer buying processes you have so far
researched in order to market the consumer product you are proposing for your final project.

Prompt: First, review Chapter 9 in your text as well as the article Stages of the Consumer Buying Process and the video 7 Tips for Good Survey Questions. Next,
prepare a presentation that lists and briefly explains each stage of the consumer buying process. Define the marketing strategy used within each stage of the
process regarding your chosen market segment. Finally, identify which specific stages of the process will be most effective for your consumer segment.

Specifically, the following critical elements must be addressed:

III. Consumer Buying Process

A. Define the stages of the consumer buying process.
B. Analyze a marketing strategy that can be used for each stage of the consumer buying process in regard to your chosen market segment.
C. Determine the specific stages of the consumer buying process for which your marketing strategies can be most effective for your consumer

segment.

Using the speaker notes, provide any additional details of importance regarding the bullet points you listed on each slide to further explain the information.

Instructor feedback on this milestone should be incorporated into your next milestones and into the final project.

Rubric

Guidelines for Submission: Milestone Two should be a minimum 3-slide PowerPoint presentation with audio or speaker notes included. Citations should be
provided in APA format as needed.

For help with PowerPoint and preparing your slideshow, visit Infobase, or the Microsoft PowerPoint help center.

Please note that the grading rubric for this milestone submission is not identical to that of the final project. The Final Project Rubric will include an additional
“Exemplary” category that provides guidance for how you can go above and beyond “Proficient” in your final submission.

Critical Elements Proficient (100%) Needs Improvement (75%) Not Evident (0%) Value
Consumer Buying

Process: Stages
Defines the stages of the consumer
buying process

Identifies the stages, but does not
identify all stages or does not define
the steps, or definition is not cogent or
inaccurate

Does not define the stages of the
consumer buying process

30

Consumer Buying
Process: Marketing

Strategy

Analyzes a marketing strategy that can
be used for each stage of the
consumer buying process in regard to
market segment

Analyzes marketing strategies, but
does not address each step of the
process or is misaligned with market
segment or description is not cogent

Does not describe marketing strategies
for stages of the consumer buying
process

30

Consumer Buying
Process: Buying

Process

Determines stages in the consumer
buying process where marketing
strategies can be most effective given
the selected consumer segment

Determines stages in the consumer
buying process where identified
marketing strategies can be most
effective, but is not aligned with the
selected consumer segment

Does not determine stages where
identified marketing strategies would
be most effective

30

Articulation of
Response

Submission has no major errors related
to citations, grammar, spelling, syntax,
or organization

Submission has major errors related to
citations, grammar, spelling, syntax, or
organization that negatively impact
readability and articulation of main
ideas

Submission has critical errors related
to citations, grammar, spelling, syntax,
or organization that prevent
understanding of ideas

10

Total 100%

1

Dallas City Hall

Name

Professor

Institution

Course

Date

2

One of the buildings that I chose from Leoh Ming’s architect works is the Dallas City

building located in Dallas, USA. I have chosen the building due to its unique structure and its

intention to serve as the administrative centre for Dallas’ municipal administration. However,

the structure slopes at a 34-degree inclination, each of the building’s seven above-grade levels

are 9.5-feet wider from the one below it. This sloping façade interacts only with buildings on

either side that face downtown and offers shelter from the elements and the Texas sun.

Although the foundation and basement levels are far more extensive than the visible

footprint of the building, they are hidden behind the sloping façade and extend well beyond

it. Two hundred thirty feet in width, the cantilevered roof spans 200 feet (61 meters), the

ground level is 126 feet in width, and the basement is 230 feet. Three cylindrical pillars that

seem to prop up the structure were constructed due to the Mayor’s reaction to the apparent

upper of the building’s form. In addition to providing cosmetic support, these pillars do not

carry the structure’s weight. The design and construction of the structure and the Park Plaza

and the garage came to more than $70 million in total.

When designing City Hall, Pei employed cast-in-place concrete structures for the

interior and outside of the building and the building and park itself. Each story is

approximately nine feet larger than that below it, with the building tilting outward at a 34-

degree angle. The symbolic logic and functional logic are both present in the 560-foot-long

from. The building has utilized the following principles in the construction: attraction and

engagement, visibility, nature and sustainability, public transportation as well as integration.

Wu Ying’s scholarly work focuses on the adaptability of construction materials in

exterior building design. To enhance the building’s exterior, adaptation research in the usage

of construction materials must be prioritized. This Research examines building materials’

3

flexibility in external design form to increase current building engineering look, project

value, and building field production efficiency. The article will help me understand more

about the Dallas City building (Ying, 2018).

The scholarly book by Perez and Perini covers nature-Based Approaches to Urban

and Residential Sustainability. Discusses the basic principles of natural components in the

building design and the tactics required to incorporate them into buildings and towns. The

three parts explore the quantifiable advantages, outcomes, concerns and challenges of

integrating nature into our constructed environment (Perez & Perini, 2018).

The scholarly article by (Puspitasari & Kwon, 2020) analyses the skyline and tall

buildings’ visibility using a dependable approach. According to the Research, towering

building clusters may be studied by looking at all unimpeded views from adjacent streets and

their effect on the skyline using Jakarta as an example.

The article by (Abdelhameed & Saputra, 2020) describes how the architectural design

incorporates building services. Specifically, the study examines the relevance of building

service systems (BSS) and how they should be considered throughout the early architectural

design stages. These systems should be included in the building from the early design stages

to save money and avoid costly and time-consuming adjustments.

4

References

Abdelhameed, W., & Saputra, W. (2020). Integration of building service systems in

architectural design. Journal of Information Technology in Construction, 25, 109–

122. https://doi.org/10.36680/j.itcon.2020.007

Perez, G., & Perini, K. (2018). Nature-Based Strategies for Urban and Building

Sustainability. In Google Books. Butterworth-Heinemann. https://books.google.co.ke/

books?

id=_wIxDwAAQBAJ&dq=nature+and+sustainability+of+a+building&hl=en&sa=X&

ved=2ahUKEwjrhdKOmZ_2AhVPUxoKHeBJDsUQ6AF6BAgKEAI

Puspitasari, A. W., & Kwon, J. (2020). A reliable method for visibility analysis of tall

buildings and skyline: a case study of tall buildings cluster in Jakarta. Journal of

Asian Architecture and Building Engineering, 1–12. https://doi.org/

10.1080/13467581.2020.1787839

Ying, W. (2018). Research on the Adaptability of Building Materials Application in Exterior

Exterior Design of Buildings. IOP Conference Series: Earth and Environmental

Science, 189, 032009. https://doi.org/10.1088/1755-1315/189/3/032009

Coca Cola
Megan George

Consumer segment

! The Coca Cola understands the needs of the
customers.

! It develops a business strategy that aligns with
the expected consumer behavior.

! Primary consumers or target market (consumers
aged 10-25 years).

! Secondary consumers (aged 25-40 years) (Wang,
2021).

Resources

! Consumer behavior information can be sourced
from resources such as:

! Social media platforms.
! Focus groups and surveys.
! Customer reviews
! Competitor analysis.

Secondary research

! Scholarly reviewed articles and journal articles are
used in studying the characteristics of Coca Cola’s
consumer segment.

! Characteristics of the consumer segment:
! Highly influenced into adapting a given

consumption behavior.
! Majority have varying purchasing power with

differences in level of income.
! Prefer trending fashion or newly introduced products

(Melancon & Dalakas, 2018).

Segmentation strategies

! There are various strategies the Coca Cola Company
can segment the market:

! Demographic such as age, income, occupation and
income.

! Geographic segmentation: based on the location of
the customer.

! Psychographics: based on hobbies and interest
! Behavioral; strategy: based on behavioral patterns as

studies from the resources.

Behavioral segmentation

! This segmentation strategy is based on consumer
behavior.

! Consumer aged (20-45) are affected by factors
such as income, interests, age.

! These factors affect their consumer patterns.
! Behavioral segmentation would assist in

implementing the best offer in terms of marketing
mix.

Selected consumer segment

! Segment: Low income, highly literate adults
aged 25-40 years

! The segment is highly price sensitive due to
limited purchasing power.

! The segment understands the quality standards
of the product.

! The segment has information on prices (De et al,
2021).

Research needs

! Impact of technology: helps determine needed
differentiation strategies.

! Effect of change in income: helps in
understanding expected changes in demand.

! Effect of competition and pricing: helps
determine the ability to switch to competitors.

References 


Wang, J. (2021, October). How Coca Cola and Pepsi Use Segmentation
in Consumer Product Industry. In 2021 International Conference on
Public Relations and Social Sciences (ICPRSS 2021) (pp. 866-870).
Atlantis Press.
Melancon, J. P., & Dalakas, V. (2018). Consumer social voice in the age
of social media: Segmentation profiles and relationship marketing
strategies. Business Horizons, 61(1), 157-167.
De Villiers, R., Tipgomut, P., & Franklin, A. (2020). International market
segmentation across consumption and communication categories:
Identity, demographics, and consumer decisions and online habits.

2/3/2022

1

Your Research Paper

• Use 8 ½ by 11” white paper, with margins
of 1” (or 1 ¼”)

• Double space EVERYTHING

• Font should be pica 10 pitch or Times
Roman 12 pitch

• Single spaces between sentences

• Page numbers in upper right hand corners

How to set up your paper in APA

2/3/2022

2

• Title Page
• Abstract
• Introduction
• Review of Literature
• Method

– Participants
– Apparatus and Measures
– Design
– Procedures

• Expected Results
• Reference Section

Key Elements

Title Page

2/3/2022

3

• One paragraph

• 150 – 250 words

• Format
– Purpose of Study

– Participants

– Methods and Materials

– Anticipated results

Abstract

2/3/2022

4

• Sets the stage for the project
• Creates reader interest in the topic
• Establishes the issues or concerns that

leads to the study
• Conveys information about the problem
• Places the study within the larger context
• Reaches out to a specific audience

Introduction

• The primary purpose of a review of
literature is to demonstrate why your study
is necessary.

• What research has been performed by
others that relates to your topic

Review of Literature

2/3/2022

5

• Review
– Setting
– Population

– Methods
– Outcomes

• Evaluate
– Relations

– Contradictions
– Gaps

– Inconsistencies

Review and Evaluate

• Corrigan, Rowan, Green, Lundin, River, Uphoff-
Wasowski, White and Kubiak (2002) conducted
two studies examining the causal processes in
contact, fear and rejection. Corrigan et al. posited
two models to account for stigmatizing reactions.
In the first model, labeled personal responsibility,
beliefs about personality responsibility influences
both the level of pity and anger displayed toward
mental patients. Additionally, the variables of pity
and anger influence helping behavior. In the
second model, labeled dangerousness, perceived
dangerousness influences fear of mental patients,
which in turn influences the avoidance of the
mentally ill.

An Excerpt from a Review of Literature

2/3/2022

6

• Taken as a whole, it appears that exposing
these myths as myths increases the
acceptance of the mentally ill and that staged
contact with a mentally person to expose
myths has an even more powerful effect.
Caution must be advised, though; Martin et
al.’s (2002) and Alexander and Link’s (2003)
studies and the first study of Corrigan et al.
(2002) were based upon paper and pencil
methodologies. And while Corrigan et al.’s
(2002) second study involved staged Myths
of violence 6 presentations, it was conducted
in a college setting with a college sample.

Another Excerpt from the Same Review

• Participants
– Who will be in your study?

– What population did you use?

– Were there any restrictions in the nature of
your participant pool?

Method

2/3/2022

7

• Total number of participants and the number
assigned to each condition

• Major demographic characteristics of the
participants (age, sex, etc.)

• Way the participants were selected
• Was the selection restricted in some way?

– All counseling majors
– Only women
– Only deaf

• How were the participants assigned?

Participant Information

Twenty-seven students from South
University (12 women and 15 men) ranging
in age from 17 to 43 years old, voluntarily
participated in this experiment. There were
9 participants randomly assigned to each of
the three conditions. Informed consent was
obtained from all participants.

Example:

2/3/2022

8

Sixteen undergraduates at South University
(12 males and 4 females) participated in
exchange for partial course credit. All
participants performed in the same way.
Data from 5 subjects who indicated that they
did not learn English before 5 years of age
were excluded from all analyses. No color-
blind subjects were included in any of the
experiments. Informed consent was
obtained from all participants.

Example:

• Apparatus/Materials
– Tells the reader what equipment and tools you

used in your experiment and to acquire the
data

Method

2/3/2022

9

Materials

A survey was constructed and used that
contains six simple yes or no questions
dealing with honesty, cheating, stealing, and
not getting caught (see appendix). A
Monopoly game board was used for
demonstrating question one.

Example:

Materials

The Social Phobia Scale was utilized in this study
(see Appendix). It is a questionnaire consisting of 15
items in which the subject is asked to put a
checkmark in the blank in front of any item that is
applied to them in the last six months. It was created
as an assignment in Psychological Statistics and
Measurements class at South University. Internal
reliability is been determined for the scale, and
content and construct validity have been established
as well.

Example:

2/3/2022

10

Materials
A website was created for presenting various
surveys (see appendix). The Keirsey
Temperament Sorter (Keirsey, 1998b) and the
Keirsey Character Sorter (Keirsey, 1998c) were
utilized to measure personality type. Two other
surveys developed by the researcher were also
administered: a short demographic survey (see
Appendix) and an assessment of the degree of
domestic violence experienced by each
participant (see appendix). All the surveys were
conducted on the computer with the results
recorded on an answer sheet (see appendix).

Example:

• What type of design did you use?
– Within subjects

• Counterbalancing

– Between subjects

– Quasi-experimental

– Experimental

– Correlational

– Survey/Descriptive

Design

2/3/2022

11

• Variables
– What is your independent variable (s)? How

many levels?

– What it is your dependent variable (s)?

• Threats to internal or external validity
– What?

– How you intend to control for them

Design

• Provides the reader with a summary of each step in the
execution of the research

• Blue Print of your data collection process
• Should be sufficiently detailed so that anyone reading your

paper could conduct the study as you intended
• Provides a verbal record telling the reader

– Who

– What

– Where

– When

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Additional Help and Assistance

Host-Microbe Coevolution: Applying Evidence from Model
Systems to Complex Marine Invertebrate Holobionts

Paul A. O’Brien,a,b,c Nicole S. Webster,b,c,d David J. Miller,e,f David G. Bournea,b,c

aCollege of Science and Engineering, James Cook University, Townsville, QLD, Australia
bAustralian Institute of Marine Science, Townsville, QLD, Australia
cAIMS@JCU, Townsville, QLD, Australia
dAustralian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
eARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
fCentre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia

ABSTRACT Marine invertebrates often host diverse microbial communities, making
it difficult to identify important symbionts and to understand how these communi-
ties are structured. This complexity has also made it challenging to assign microbial
functions and to unravel the myriad of interactions among the microbiota. Here we
propose to address these issues by applying evidence from model systems of host-
microbe coevolution to complex marine invertebrate microbiomes. Coevolution is
the reciprocal adaptation of one lineage in response to another and can occur
through the interaction of a host and its beneficial symbiont. A classic indicator of
coevolution is codivergence of host and microbe, and evidence of this is found in
both corals and sponges. Metabolic collaboration between host and microbe is of-
ten linked to codivergence and appears likely in complex holobionts, where micro-
bial symbionts can interact with host cells through production and degradation of
metabolic compounds. Neutral models are also useful to distinguish selected mi-
crobes against a background population consisting predominately of random associ-
ates. Enhanced understanding of the interactions between marine invertebrates and
their microbial communities is urgently required as coral reefs face unprecedented
local and global pressures and as active restoration approaches, including manipula-
tion of the microbiome, are proposed to improve the health and tolerance of reef
species. On the basis of a detailed review of the literature, we propose three re-
search criteria for examining coevolution in marine invertebrates: (i) identifying sto-
chastic and deterministic components of the microbiome, (ii) assessing codivergence
of host and microbe, and (iii) confirming the intimate association based on shared
metabolic function.

KEYWORDS codivergence, coevolution, marine invertebrates, microbiome,
phylosymbiosis

Coevolution theory dates back to the 19th century (box 1), and coevolution iscurrently referred to as the reciprocal evolution of one lineage in response to
another (1). This definition encompasses a broad range of interactions such as predator-
prey, host-symbiont, and host-parasite interactions or interactions among the members
of a community of organisms such as a host and its associated microbiome (1, 2). In the
case of host-microbe associations, this has produced some of the most remarkable
evolutionary outcomes that have shaped life on Earth, such as the eukaryotic cell,
multicellularity, and the development of organ systems (3, 4). It is now recognized that
microbial associations with a multicellular host represent the rule rather than the

Citation O’Brien PA, Webster NS, Miller DJ,
Bourne DG. 2019. Host-microbe coevolution:
applying evidence from model systems to
complex marine invertebrate holobionts. mBio
10:e02241-18. https://doi.org/10.1128/mBio
.02241-18.

Editor Danielle A. Garsin, University of Texas
Health Science Center at Houston

Copyright © 2019 O’Brien et al. This is an
open-access article distributed under the terms
of the Creative Commons Attribution 4.0
International license.

Address correspondence to David G. Bourne,
david.bourne@jcu.edu.au.

Published 5 February 2019

MINIREVIEW
Host-Microbe Biology

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exception (4), but in complex associations of that kind, the extent to which coevolution
operates is often unclear.

BOX 1: A BRIEF HISTORY OF COEVOLUTION
Charles Darwin once explained the sudden and rapid diversification of flowering

plants as an “abominable mystery,” since it could not be explained by traditional
views of evolution alone (5). While his correspondent Gaston de Saporta speculated
that a biological interaction between flowering plants and insects might be the
cause of the phenomenon, it was not until nearly 100 years later that the concept of
coevolution developed. In a pioneering study, Ehrlich and Raven (6) observed that
related groups of butterflies were feeding on related groups of plants and specu-
lated this was due to a process for which they coined the name “coevolution.” Using
butterflies, they argued that plants had evolved mechanisms to overcome predation
from herbivores, which in turn had evolved new ways to prey on plants. Decades on,
the introduction of phylogenetics has shown that plants evolved in the absence of
butterflies, which colonized the diverse group of plants after their chemical defenses
were already in place (7). Nevertheless, the theory of coevolution was endorsed, and
two important points came to light. First, care must be taken when inferring
coevolution from seemingly parallel lines of evolution, and where possible, diver-
gence times and common ancestry should be included. Second, coevolution can
occur between communities of organisms (“guild” coevolution), as observed in the
case of flowering plants, where predation and pollination from a wide variety of
insects likely influenced the diversification of angiosperms (8).

Since coevolution can occur across multiple levels of interactions, multiple theories
have also developed. The Red Queen theory is based on the concept of antagonistic
coevolution and assumes that an adaptation that increases the fitness of one species
will come at the cost to the fitness of another (9). This type of coevolution has been
most pronounced in host-parasite interactions, where the antagonistic interactions are
closely coupled (10). However, coevolutionary patterns may also arise in the case of
mutualistic symbioses, which require reciprocal adaptations to the benefit of each
partner (11). Mutualistic coevolution is associated with a number of key traits that are
discussed further in this review, such as obligate symbiosis, vertical inheritance, and
metabolic collaboration. Third, coevolution has also recently been placed in context of
the hologenome theory (12), which suggests that the holobiont can act as a unit of
selection (but not necessarily as the primary unit) since the combined genomes
influence the host phenotype on which selection may operate (13, 14). However,
hologenome theory also acknowledges that selection acts on each component of the
holobiont individually as well as in combination with other components (including the
host). Thus, the entity that is the hologenome may be formed, in part, through
coevolution of interacting holobiont compartments, in addition to neutral processes
(12).

Given the ubiquitous nature of host-microbe associations and the huge metabolic
potential that microorganisms represent, it is not surprising that evidence of host-
microbe coevolution is emerging. Model representatives of both simple and complex
associations are being used to study coevolution, allowing researchers to look for
specific traits, signals, and patterns (1, 15). A well-known model system is the pea-aphid
and its endosymbiotic bacteria in the genus Buchnera. This insect has evolved special-
ized cells known as bacteriocytes to host its endosymbionts, which in turn synthesize
and translocate amino acids that are missing from the diet of the pea aphids (16).
Amino acid synthesis occurs through intimate cooperation between host and symbiont,
with some pathways missing from the host and some from the symbiont, such that the
relationship is obligate to the extent that the one organism cannot survive without the
other (17). The human gut microbiome has been extensively studied in complex
systems and has been shown to be intimately associated with human health. Gut

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microbes have been shown to be linked with human behavior and development
through metabolic processes, such as microbial regulation of the essential amino acid
tryptophan (18, 19). The human microbiome contains around 150-fold more nonre-
dundant genes than the human genome (20), and the metabolic capacity of microbes
residing in the intestine is believed to have been a driving evolutionary force in the
host-microbe coevolution of humans (2). In these examples, as well as many others
(21–23), both host and symbiont evolved to maintain and facilitate the symbiosis.
Furthermore, phylogenies of host and symbiont in these systems are often mirrored,
indicating that host and symbiont are diverging in parallel (16, 24, 25), a phenomenon
known as codivergence (26).

In the marine environment, invertebrates can host microbial communities as simple
and stable as that of the pea aphid or as complex and dynamic as that of the human
gut (Fig. 1). The Hawaiian bobtail squid, for example, maintains an exclusive symbiosis
with a single bacterial symbiont which it hosts within a specialized light organ (27). On
the other hand, corals host enormously diverse microbial communities, comprising
thousands of species-level operational taxonomic units (OTUs), which are often influ-
enced by season, location, host health, and host genotype (28–31). Marine sponges also
host complex microbial communities with diversity comparable to that of corals (32)
but with associations that are generally far more stable in space and time (33).
Less-diverse microbial communities are found in the sea anemone Aiptasia, where the
number of OTUs is generally in the low hundreds (34). Due to the close taxonomic
relationship of Aiptasia with coral and its comparatively simple microbial community, it
has been proposed as a model organism for studying coral microbiology and symbiosis
(34). Some marine invertebrates also include species along a continuum of microbial
diversities. Ascidians, for example, have been shown to host fewer than 10 (Polycarpa
aurata) or close to 500 (Didemnum sp.) microbial OTUs within their inner tunic (35).
Furthermore, species with low microbial diversity such as P. aurata can exhibit high
intraspecific variation, with as few as 8% of OTUs shared among individuals of the same
species (35). Taken together, the data from those studies highlight the vast spectrum
of associations that marine invertebrates form with microbial communities in terms of
diversity, composition, and stability (Fig. 1).

While previous research has provided a good understanding of the composition of
marine invertebrate microbiomes, our understanding of how the microbiome interacts
with the host, and of the potential to coevolve, is far more limited. Moreover, the

FIG 1 Spectrum of microbial diversity associated with different compartments of marine invertebrates. Microbial associations may involve a single symbiont
in a specialized organ or over 1,000 operational taxonomic units (OTUs) associated with tissues. The levels of OTUs reported in the figure represent the highest
recorded in the referenced study for that species. Reported levels of diversity may differ significantly within the same species across different studies.

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increasing number of studies generating tremendous volumes of host-associated
microbiome sequence data requires theoretical development to interpret these rela-
tionships. Coevolved microbial symbionts are presumed to be intimately linked with
host fitness and metabolism (36); therefore, understanding these relationships in
marine invertebrates will have direct implications for health and disease processes in
these animals. Three research criteria arise for examining coevolution in marine inver-
tebrates: (i) identifying stochastic and deterministic microbial components of the
microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming an
intimate association between host and microbe related to shared metabolic function
(metabolic collaboration). While each of these criteria may be fulfilled without the
involvement of coevolution (26, 37, 38), evidence of their existence in combination
provides a strong basis for establishing coevolution patterns (Fig. 2). This review
positions these three criteria in coevolution as representing a complementary approach
to the study of complex marine invertebrate microbiomes by drawing from examples
of model systems. Focussing on keystone coral reef invertebrates, this review also
evaluates the current evidence for each criterion. Finally, while parasites and pathogens
also contribute to host coevolution, the focus of this review is mutualistic symbionts;
thus, pathogens and parasitism are not discussed.

BOX 2: GLOSSARY
(i) Codivergence. Two organisms which speciate or diverge in parallel as illus-

trated by topological congruency of phylogenetic trees.
(ii) Coevolution. Reciprocal adaptation of one (or more) lineage(s) in response to

another (or others).
(iii) Holobiont. A host organism and its associated microbial community.
(iv) Hologenome. The collective genomes of a host and its associated microbial

community, which may act as a unit of selection or at discrete levels.
(v) Metabolic collaboration. Two or more oganisms that are linked through

metabolic interactions, generally to the benefit of one another.
(vi) Metagenome. The collective microbial genes recovered from an environmen-

tal sample, usually predominantly prokaryotic.
(vii) Metatranscriptomics. Quantification of the total microbial mRNA in a sample

as an indication of gene expression and active microbial functions.
(viii) Microbiome. The total genetic make-up of a microbial community associated

with a habitat.
(ix) Microbiota. The community of microorganisms residing in a particular habitat,

usually a host organism.
(x) Phylosymbiosis. The rentention of a host phylogenetic signal within its

associated microbial community.
(xi) Virome. The total viral genetic content recovered from an environmental

sample.

UNTANGLING PATTERNS OF HOST-MICROBE COEVOLUTION IN A WEB OF
MICROBES

(i) Phylosymbiosis and neutral theory—identifying stochastic and determinis-
tic components of the microbiome. Host-microbe coevolution may occur to some
degree at the level of the hologenome, i.e., reciprocal evolution of the host genome
and microbiome (12). Therefore, it is necessary to understand microbial community
structure and population dynamics within the host environment. This may illustrate (i)
that the microbiome associated with a host is structured through phylogenetically
related host traits and may therefore retain a host phylogenetic signal (phylosymbiosis)
and (ii) that certain microbes deviate from the expected patterns of neutral population
dynamics, i.e., stochastic births and deaths and immigration. It is likely that phylosym-
biosis and neutral population dynamics are linked; therefore, their potential to con-
tribute to coevolution is discussed together.

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Homocysteine + Serine
(host diet & metabolism)

Cystathionine B-synthase
(symbiont enzyme)

Cystathionine

Cystathionine y-lyase
(host enzyme)

Cysteine

S-H
CH2

C COOH H2N
H

Bacteria spp. 1

Host spp. A

d)

Host phylogeny Microbial dendrogram
Host species

A

B

C

D

a)

b)

Host phylogeny Microbial phylogeny

Bacteria spp. 1

A

B

C

D

Relative abundance of
microbes in host sample

Fr
eq

ue
nc

y
of

m
ic

ro
be

s
in

h
os

t Bacteria spp. 1

Bacteria spp.2
Low High

0

1

c)

FIG 2 Hypothetical scenario addressing three criteria for host-microbe coevolution in species A to D. (a) Phylosymbiosis
shown through hierarchical clustering of the microbial community, resulting in a microbial dendrogram which mirrors host
phylogeny. (b) Neutral model showing the expected occurrence of microbes based on neutral population dynamics (blue
line). As the relative abundance increases, so too does the occurrence in host samples. The members of bacterial species
group 1 (Bacteria spp. 1) are therefore more abundant than would be expected by chance and may indicate active selection,
while the members of Bacteria spp. 2 are less abundant. (c) Codivergence of the members of Bacteria spp. 1 with their hosts.
The members of Bacteria spp. 1 are found within the microbial community of each host species and appear to be actively
selected for. Their phylogeny indicates a host split at the strain level followed by diversification within each host species.
Congruence between host and microbial lineages suggests important host-microbe interactions and warrants further
investigation. (d) Metabolic collaboration between the members of Host spp. A and those of Bacteria spp. 1. Fluorescence
in-situ hybridization (FISH) confirms that the members of Bacteria spp. 1 are located within bacteriocyte cells in the tissues
of Host spp. A. Genome and transcriptome data for each species suggest that the amino acid cysteine is produced by the
activity of a metabolic pathway shared between host and microbe. In corals of the genus Acropora, for example, the
genome is incomplete with respect to biosynthesis of cysteine and represents a potential pathway for collaborations of host
and microbe (101). Hypothetically, the amino acids homocysteine and serine (potentially sourced from host diet and
metabolism) are combined to form cystathionine through the enzyme cystathionine V synthase (provided by the host’s
endosymbiont). The host enzyme cystathionine �-lyase then breaks down cystathionine to form cysteine.

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The term “phylosymbiosis” is not intended to imply coevolution (12, 38); however,
coevolution of a host and microbiome may reinforce patterns of phylosymbiosis. There
are many host traits that correlate with host phylogeny, some of which can act as
environmental filters, preventing the establishment of microbes in the host environ-
ment. Thus, neutral population dynamics, with host traits acting as an ecological filter
to microbial immigration, may be sufficient to result in phylosymbiotic patterns (39, 40).
However, host traits are not static; thus, the evolution of these microbial niches may
further drive the radiation of the microbes that reside within them. In turn, the
continuous colonization over many generations of a microbial community likely adds
to the selective pressure on host traits. Therefore, ecological filtering of microbes
through host traits and coevolution of a host and microbiome need not be mutually
exclusive in the appearance of phylosymbiosis (39). Moreover, assessing patterns of
phylosymbiosis and neutral population dynamics also allows the detection of microbes
that deviate from these patterns and may identify important microbial species that are
actively selected for (or against) by the host. In this context, neutral models can
simulate expected microbial abundance, allowing easier detection of microbes that do
not fit these patterns (41). This reasoning justifies consideration of phylosymbiosis and
microbial population dynamics in assessing coevolution in complex holobionts.

Patterns of phylosymbiosis are frequently detected in complex holobionts. One
particular study tested for phylosymbiosis across 24 species of terrestrial animals from
4 groups that included Peromyscus deer mice, Drosophila flies, mosquitos, and Nasonia
wasps and an additional data set of 7 hominid species (42). Since these animals (with
the exception of hominids) could be reared under controlled laboratory conditions,
environmental influences could be eliminated, leaving the host as the sole factor
influencing the microbial community. Under these conditions, phylosymbiotic patterns
were clearly observed for all five groups, with phylogenetically related taxa sharing
similar microbial communities and microbial dendrograms mirroring host phylogenies.
Similar patterns of phylosymbiosis have been observed in a growing number of
terrestrial systems, including all five gut regions in rodents (43), the skin of ungulates
(44), the distal gut in hominids (45), and roots of multiple plant phyla (46), providing
evidence that such patterns are common among host-associated microbiomes.

In the marine environment, two major studies, one involving 236 colonies across 32
genera of scleractinian coral collected from the east and west coasts of Australia (47)
and the other involving 804 samples of 81 sponge species collected from the Atlantic
Ocean, Pacific Ocean, and Indian Ocean and the Mediterranean Sea and Red Sea (32),
have provided the most convincing examples of phylosymbiosis. Both studies found a
significant evolutionary signal of the host with respect to microbial diversity and
composition. Specifically, mantel tests were used to delineate the finding that closely
related corals and sponges hosted more extensively similar microbial communities in
terms of composition than would be expected by chance. In the case of corals, the
similarity was seen in the skeleton and, to a lesser extent, in the tissue microbiome,
while the mucus microbiome was more highly influenced by the surrounding environ-
ment (47). However, both studies found that host species was the strongest factor in
explaining dissimilarity among microbial communities. Additional studies on both cold
water and tropical sponges have found similar phylogenetic patterns within the
microbiome of the host species (48, 49). Together, these results suggest that host
phylogeny (or associated traits) has a significant role in structuring associated microbial
communities, although there are additional factors related to host identity (and unre-
lated to phylogeny) that also likely play a major role.

Most studies to date have focused on the microbes that adhere to these patterns of
phylosymbiosis, though more-useful information arguably could be determined from
the microbes that do not. Since phylosymbiosis is a pattern that shows correlations
between microbiome dissimilarity and host phylogeny, it does not indicate active
microbial selection or cospeciation (38), and the species that deviate from these
patterns would be interesting targets for studies of codivergence and metabolic
collaboration (see below). Neutral models have been applied to three species of

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sponges, a jellyfish, and a sea anemone, and while neutral models have been shown to
fit well to the expectation of microbial abundance in sponges (which also show
phylosymbiosis), jellyfish and sea anemone microbiomes were found to be associated
with a higher level of nonneutrality (40). Potential reasons for nonneutrality include the
presence of a more sophisticated immune system in cnidarians that provides active
selection on certain microbial taxa and that the microbiomes in such cases are more
transient or a combination of the two. In summary, neutral population dynamics filtered
through phylogenetically related host traits likely result in, or at least contribute to, the
observed patterns of phylosymbiosis. This does not necessarily mean that the pattern
is unimportant or is not contributing to coevolution at the hologenome level, and it
may be that the communities of microbes that follow these patterns are responsible for
broad ecological functions (50). On the other hand, microbes that deviate from these
patterns may be responsible for more-specific functions and are of high interest to
those trying to identify symbionts and coevolution at the microbial species or strain
level.

(ii) Codivergence—microbial phylogeny and host phylogeny are congruent.
The second criterion in assessing host-microbe coevolution is that of whether individ-
ual microbial lineages and their hosts have matching phylogenies (22, 24, 51). Codi-
vergence implies a tightly coupled, long-term interaction between two species and can
potentially identify beneficial symbionts (or parasites) that have coevolved with the
host (26). However, it is also important that codivergence can arise due to processes
other than coevolution, such as one species adaptively tracking another, which would
imply that the evolution is not reciprocal, or two species responding independently to
the same speciation event or environmental stress (37). In known cases of coevolution,
phylogenies of hosts and their microbial symbionts are congruent (16, 51, 52). However,
in complex and uncharacterized systems, this strategy can be reversed to identify
potential symbionts. Therefore, the main value of investigating codivergence in com-
plex associations is to identify those specific microbes on which to focus further
attention.

Codivergence has been demonstrated in the case of Hydra viridissima, a freshwater
relative of marine cnidarians, and its photosymbiont Chlorella (53). In this system,
photosynthetically fixed carbohydrates from Chlorella are transported to its host (54),
and phylogenetic analysis of 6 strains of H. viridissima and their vertically transmitted
symbionts revealed clear congruency of host and symbiont topologies (55). In more-
complex systems, patterns of codivergence have been illustrated in the gut microbiota
of hominids (25). Analysis of fecal samples from humans, wild chimpanzees, wild
bonobos, and wild gorillas showed that four clades of bacteria from the dominant
families Bacteroidaceae and Bifidobacteriaceae codiverged with host phylogeny. Impor-
tantly, this example illustrates one possible way of identifying codivergence in complex
holobionts where the symbionts are unknown. Since bacteria from the families Bacte-
roidaceae, Bifidobacteriaceae, and Lachnospiraceae are known to dominate the gut of
hominids, multiple primer sets targeting each individual family were utilized, and
phylogenetic analyses of the families were completed independently. Furthermore,
instead of using the relatively slowly diverging 16S rRNA gene, the fast-evolving and
variable gene encoding DNA gyrase subunit B was used for bacterial phylogenetics.
Similar methods may be applied to complex marine invertebrates such as coral and
sponges, where 16S rRNA gene studies have identified prominent bacteria.

Within complex marine invertebrate holobionts, codivergence has been most clearly
demonstrated in cold-water sponges in the family Latrunculiidae. The microbiomes of
six species within this family were dominated by a single betaproteobacterial OTU, and
the phylogeny of this OTU was highly congruent with that of the host (56). Further-
more, gene expression analysis suggested that the dominant betaproteobacteria are
active members of the microbiome rather than dormant or nonviable members;
however, whether or not this potential symbiont and its host participate in metabolic
collaboration is unknown, highlighting an example warranting further investigation.
The microbiomes of many other marine invertebrates are dominated by members of

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the genus Endozoicomonas (57). A pan-genomic analysis of the genomes of seven
Endozoicomonas strains representing a broad range of hosts (corals, sponges, and sea
slugs) provided some evidence for codivergence (58). Strikingly, the two closely related
corals Stylophora pistillata and Pocillopora verrucosa hosted Endozoicomonas with
highly similar genomes. A second, large-scale study (47) found that Endozoicomon

Running Head: RESEARCH PAPER

Mack

Title

Part 1

Name

ESSAY

Natural experiments and long-term

monitoring are critical to understand and

predict marine host–microbe ecology and

evolution

Matthieu LerayID
1‡*, Laetitia G. E. WilkinsID

2¤‡
, Amy ApprillID

3
, Holly M. BikID

4
,

Friederike Clever
1,5

, Sean R. ConnollyID
1
, Marina E. De León

1,2
, J. Emmett DuffyID

6
,

Leïla Ezzat7, Sarah Gignoux-WolfsohnID8, Edward Allen Herre1, Jonathan Z. KayeID9,
David I. KlineID

1
, Jordan G. KuenemanID

1
, Melissa K. McCormickID

8
, W. Owen McMillan

1
,

Aaron O’DeaID
1,10*, Tiago J. PereiraID

4
, Jillian M. PetersenID

11
, Daniel F. PetticordID

1
,

Mark E. Torchin
1
, Rebecca Vega ThurberID

12
, Elin VidevallID

13,14
, William T. WcisloID

1
,

Benedict YuenID
11

, Jonathan A. EisenID
2,15,16

1 Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama, 2 UC Davis Genome

Center, University of California, Davis, Davis, California, United States of America, 3 Marine Chemistry and

Geochemistry Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United

States of America, 4 Department of Marine Sciences and Institute of Bioinformatics, University of Georgia,

Athens, Georgia, United States of America, 5 Department of Natural Sciences, Manchester Metropolitan

University, Manchester, United Kingdom, 6 Tennenbaum Marine Observatories Network, Smithsonian

Environmental Research Center, Edgewater, Maryland, United States of America, 7 Department of Ecology,

Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, California, United

States of America, 8 Smithsonian Environmental Research Center, Edgewater, Maryland, United States of

America, 9 Gordon and Betty Moore Foundation, Palo Alto, California, United States of America,

10 Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy,

11 Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria,

12 Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America,

13 Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, United

States of America, 14 Department of Ecology and Evolutionary Biology, Brown University, Providence,

Rhode Island, United States of America, 15 Department of Evolution and Ecology, University of California,

Davis, Davis, California, United States of America, 16 Department of Medical Microbiology and Immunology,

University of California, Davis, Davis, California, United States of America

¤ Current address: Max Planck Institute for Marine Microbiology, Department of Symbiosis, Bremen,
Germany

‡ These authors share first authorship on this work.

* leray.upmc@gmail.com (ML); odeaa@si.edu (AO)

AbstractAU : Pleaseconfirmthatallheadinglevelsarerepresentedcorrectly:
Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial

eukaryotes, and viruses that form their microbiome. Such host-associated microbes can sig-

nificantly influence the host’s physiological capacities; however, the identity and functional

role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexist-

ing in natural settings remain obscure. Also unclear is how dynamic interactions between

hosts and the immense standing pool of microbial genetic variation will affect marine eco-

systems’ capacity to adjust to environmental changes. Here, we argue that significantly

advancing our understanding of how host-associated microbes shape marine hosts’ plastic

and adaptive responses to environmental change requires (i) recognizing that individual

host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii)

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a1111111111

a1111111111

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OPEN ACCESS

Citation: Leray M, Wilkins LGE, Apprill A, Bik HM,

Clever F, Connolly SR, et al. (2021) Natural

experiments and long-term monitoring are critical

to understand and predict marine host–microbe

ecology and evolution. PLoS Biol 19(8): e3001322.

https://doi.org/10.1371/journal.pbio.3001322

Published: August 19, 2021

Copyright: This is an open access article, free of all

copyright, and may be freely reproduced,

distributed, transmitted, modified, built upon, or

otherwise used by anyone for any lawful purpose.

The work is made available under the Creative

Commons CC0 public domain dedication.

Funding: Financial support for the workshop was

provided by grant GBMF5603 (https://doi.org/10.

37807/GBMF5603) from the Gordon and Betty

Moore Foundation (W.T. Wcislo, J.A. Eisen, co-

PIs), and additional funding from the Smithsonian

Tropical Research Institute and the Office of the

Provost of the Smithsonian Institution (W.T.

Wcislo, J.P. Meganigal, and R.C. Fleischer, co-PIs).

JP was supported by a WWTF VRG Grant and the

ERC Starting Grant ’EvoLucin’. LGEW has received

funding from the European Union’s Framework

Programme for Research and Innovation Horizon

2020 (2014-2020) under the Marie Sklodowska-

Curie Grant Agreement No. 101025649. AO was

supported by the Sistema Nacional de

Investigadores (SENACYT, Panamá). A. Apprill was

supported by NSF award OCE-1938147. D.I. Kline,

M. Leray, S.R. Connolly, and M.E. Torchin were

expanding the field toward long-term, multidisciplinary research on entire communities of

hosts and microbes. Natural experiments, such as time-calibrated geological events associ-

ated with well-characterized environmental gradients, provide unique ecological and evolu-

tionary contexts to address this challenge. We focus here particularly on mutualistic

interactions between hosts and microbes, but note that many of the same lessons and

AU : Anabbreviationlisthasbeencompiledforthoseusedinthemaintext:Pleaseverifythatallentriesarecorrect:approaches would apply to other types of interactions.

Main

It is widely recognized that host-associated microbes play profound roles in the health of their

marine hosts and the ecosystems they inhabit. Although some such interactions with microbes

are transient, many are more persistent and can be generally described as symbioses. Symbio-

ses come in many flavors including parasitism, commensalism, and mutualism (see Box 1),

and, in this paper, we focus in particular on the mutually beneficial (i.e., mutualistic) subset of

such interactions involving marine hosts. Despite the wide recognition of the importance of

such mutualisms, it remains less clear how these associations scale up to drive broader ecologi-

cal and evolutionary patterns and processes. For example, the contribution of microbes to host

acclimatization and adaptation (see Box 1 for definitions) is an active new field of experimental

research with much potential. Studies, mostly conducted in controlled laboratory settings,

have evaluated the ecological costs/benefits for hosts to associate temporarily with different

microbes (e.g., corals [1–4]) or to engage in obligate intimate relationships (e.g., bobtail squid

with the bioluminescent bacteria Aliivibrio fischeri [5]).
Experimental studies are, however, intrinsically limited in several ways. They limit them-

selves to a small number of experimentally tractable hosts and microbes, and, in doing so,

fail to account for the enormous complexity of interactions and variation that exist in nature

between multiple hosts and their multitudes of associated microbes. Short-lived experiments

(e.g., days to weeks) cannot replicate the scales of time and space involved in the potential

coevolution of hosts and microbes (Box 1). Attempts to merge long-term datasets to reveal

overarching patterns (e.g., [6–9]) have provided valuable insights but are shadowed by the lim-

its and biases introduced by mixing information from different contexts or methodologies

[10]. These limitations obscure general principles on the roles (mutualistic or otherwise) of

host-associated microbes across host individuals, species, and communities [11–13].

Here, we demonstrate the value of moving beyond taxon-centric approaches to studying

host–microbe associations in their natural evolutionary and ecological context. We suggest

intensifying long-term research in well-documented “natural experiments”. Such natural

experiments, including well-calibrated geological events (e.g., vicariance and creation of novel

habitats accurately dated using fossil and geological data) and environmental gradients where

multiple hosts and associated microbes are subjected to the same range of environmental con-

ditions, can be particularly useful (Fig 1). These phenomena provide a unique framework for

comparative studies where the processes of interest occur over spatial and evolutionary time

scales that are nearly impossible to capture in laboratory experiments. The value of combining

experimental and long-term field studies at natural experiments has been recognized by ecolo-

gists [14–16]. We argue that similar approaches should be applied to the study of host–microbe

interactions. We highlight several natural experiments that can advance our understanding of

the ecological and evolutionary mechanisms shaping host–microbe interactions (with a focus

on mutualistic ones) in marine communities and ecosystems.

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supported by a Rohr Family Foundation grant for

the Rohr Reef Resilience Project, for which this is

contribution #2. This is contribution #85 from the

Smithsonian’s MarineGEO and Tennenbaum

Marine Observatories Network. The funders had no

role in study design, data collection and analysis,

decision to publish, or preparation of the

manuscript.

Competing interests: The authors have declared

that no competing interests exist.

Abbreviations: LTER, Long-Term Ecological

Research; MarineGEO, Marine Global Earth

Observatory; MBON, Marine Biodiversity

Observation Network; TEP, Tropical Eastern Pacific.

Identifying important players

Marine organisms have evolved complex structural, behavioral, and chemical mechanisms to

regulate the presence, abundance, and activity of their microbial associates. Hosts can limit

colonization by transient opportunistic microbes that would use space and resources without

providing any benefits, and some hosts can even block pathogens entirely [17–19]. Host-spe-

cific and obligate microbial associates, often called the “core microbiome” of a host population

Box 1. Definitions of key terms

Acclimatization: The process by which an organism becomes accustomed to new envi-

ronmental conditions during its lifetime.

Adaptation: A heritable trait of an organism that increases its fitness in its surrounding

environment. In comparison to acclimatization, adaptations will be passed on to the

next generation.

Convergent evolution: Independent origins of similar features in different organisms in

response to separately experiencing similar selective pressures. Importantly, conver-

gently originated features, also known as analogous features, were not present in the

common ancestor of the taxa in question.

Genetic drift: Change in the relative frequency of genotypes due to random variation in

reproduction. Such drift is more common in small populations and leads to changes in

genotype frequencies independent of adaptive forces.

Host–microbe coevolution: During host–microbe coevolution, multicellular hosts and

their associated microbes show a concerted and heritable response to an environmental

change.

Homologous recombination: The process by which two pieces or stretches of DNA that

are very similar in their sequence physically align and exchange nucleotides.

Horizontal gene transfer: The unidirectional movement of DNA, usually only small frac-

tions of a genome, from one organism to another. Though this generally occurs more

frequently within species than between, it can also occur across vast evolutionary

distances.

Metagenomics: Studies of the genetic material of communities of organisms.

Phenotypic plasticity: Phenotypic plasticity is the ability of a specific genotype to pro-

duce more than one phenotype in response to a changing environment during an indi-

vidual’s lifetime. These phenotypic changes may include an organism’s behavior,

morphology, physiology, or other features. Phenotypic plasticity is adaptive if it increases

an individual’s survival and if the ability is passed on to the next generation.

Symbioses: Symbioses are broadly defined as intimate interactions between at least two

organisms where at least one of them benefits. We focus here specifically on mutually

beneficial interactions (aka mutualisms) between multicellular eukaryotes and their

associated microbes. These interactions may include disease resistance, predator avoid-

ance, and nutrition. These interactions will ultimately increase host survival and fitness.

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Fig 1. Examples of marine natural experiments as observatories of host–microbe interactions. Regionally focused, long-term,

and taxonomically broad research programs will help fill key knowledge gaps about the nature of microbe functions and the

dynamics of host–microbe interactions in changing oceans. We highlight areas of the world’s oceans where environmental

gradients are well characterized, where the taxonomy and evolutionary history of the local host fauna and flora is already well

established, where paleoecological studies can provide important historical context, where a long-term monitoring program is

ongoing, and where there is significant research infrastructure. Long-term monitoring sites (white dots) include sites of the NSF’s

LTER Network, the Smithsonian Institution’s MarineGEO network of partners, the MBON, the AIMS, and the ASSEMBLE. (1)

NASA MODIS data; (2) Adapted from [93]; (3) Adapted from [73]; (4) Adapted from [74]; (5) Adapted from [94]; (6) Adapted

from [95]. AIMSAU : AbbreviationlistshavebeencompiledforthoseusedinFigs1and4:Pleaseverifythatallentriesarecorrect:, Australian Institute of Marine Science; ASSEMBLE, Association of European Marine Biological Laboratories;
LTER, Long-Term Ecological Research; MarineGEO, Marine Global Earth Observatory; MBON, Marine Biodiversity

Observation Network.

https://doi.org/10.1371/journal.pbio.3001322.g001

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or species, are generally assumed to play more important functional roles than opportunistic

and transient taxa [20]. This core microbiome is exemplified by an obligate nutritional micro-

bial symbiosis, in which the host relies extensively on microbial partners for survival by syn-

thesis of food, often in a nutrient-limited habitat. The host may acquire these partners

horizontally (from the surrounding environment), vertically (from the parent to the offspring),

or in both ways (mixed mode) [21]. Many evolved symbioses result in codependency; for

example, the genomes of host-associated microbes have lost genes encoding pathways that

were previously essential, such as those for motility or environmental stress responses, but that

became obsolete in obligate symbiotic lifestyles [22]. In return, hosts have evolved mechanisms

to maintain their associated microbes in stable intracellular environments and to support their

nutritional needs [23]. Some of these nutritional associations are clearly identifiable because

symbionts form massive and dense populations, sometimes only consisting of a single micro-

bial species, in or on the bodies of their hosts. Examples include photosynthetic symbioses in

cnidarians [24] and chemosynthetic symbioses in invertebrate animals such as bathymodiolin

mussels, lucinid clams, Riftia tubeworms, and Astomonema nematodes [25,26]. Although
widespread, host reliance on a single or few microbes for nutrition are the exception rather

than the rule. The vast majority of animals and plants are instead associated with a diverse

assemblage of microbes where it is challenging to differentiate between members of the core

microbiome and the myriad of transient microbes and even more challenging to determine

what, if any, key functional roles such microbes play.

Several approaches have been proposed to identify key microbes or functions within com-

plex host microbiomes (reviewed in [27]). The most common practice is to identify microbial

taxa that are consistently associated with a host population or species using marker gene

sequencing, usually above some arbitrary prevalence threshold ([28]; but see [29,30] for alter-

native methods). The prevalence of a host–microbe association is typically measured without

explicit attention to co-occurring and closely related host taxa, the surrounding environment,

or adequacy of spatial and temporal sampling. This limited sampling and lack of context, often

resulting from funding constraints, leads to several major limitations. First, a microbial taxon

can be prevalent in a host population for reasons unrelated to its functional role. For example,

it may originate from the host’s food or habitat, including seawater or sediment [31]. Second,

even the core microbiome can change over time [32]. Functionally important microbes may

fluctuate in abundance throughout host ontogeny and may also vary seasonally. Essential host-

associated microbes may be overlooked if the sampling method cannot detect low abundance

reliably, resulting in false negatives, or if sampling is sporadic, missing the life stage or season

when particular microbes are essential. Third, many studies rely upon sequencing of rRNA

genes to characterize communities, yet rRNA genes are generally too conserved to distinguish

closely related taxa and reveal little directly about genomic functional potential. Clearly, under-

standing the functional roles of host-associated microbes requires analyses that go far beyond

individual marker gene profiles and instead encompass other types of information such as

whole genomes or metagenomes, transcriptomes, metabolomes, localization, biochemistry,

and more. Fourth, taxon-focused studies may miss valuable information about interactions

that could be gleaned from broader comparative analyses. Microbes that are specific to particu-

lar host genotypes, host species, or closely related groups of hosts, indicating a shared evolu-

tionary history, are likely candidates for core microbes with specialized functions (e.g., gut

fermenters associated with herbivores). These existing limitations could be robustly circum-

vented via whole-ecosystem studies where long-term collection of comprehensive genomic-

level datasets (e.g., ‘omic scale information) would transform our understanding of host–

microbe interactions at all levels.

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To instigate this new approach, we recommend strategically intensifying research within a

few ocean regions. This entails collecting large scale data on host-associated microbes across

phylogenetically diverse sets of co-occurring host organisms, together with data on surround-

ing free-living microbes (i.e., in seawater and sediments) through time in areas where the sur-

rounding abiotic environment and community dynamics have been well characterized. A

regionally focused and coordinated approach will allow identifying environmental sources

and hosts that serve as reservoirs of key host-associated microbial taxa and genes. Long-term

investments in research on particular communities of hosts and microbes will also help estab-

lish links between changes in core microbiome composition, environmental factors, ecosystem

function, and resilience. Public archival of genomic data and samples (available for comple-

mentary analysis using emerging technologies) collected from a few intensively studied ocean

regions will foster transformative discoveries on dynamic host–microbe relationships. Habi-

tat-forming corals, sponges, seagrasses, and mangrove trees are important focal groups, since

breakdowns in the associations between these species and their microbiomes likely dispropor-

tionately influence other taxa and ecosystem functions. However, this should not come at the

expense of research on more inconspicuous and overlooked, yet functionally important taxa

that comprise the majority of the oceans’ biological diversity (e.g., small fish that fuel marine

food webs [33] and urchins and crustaceans that feed on algae that can displace corals [34]).

Systematic biases toward studying certain taxa (vertebrates, species with large body sizes,

charismatic fauna), partly caused by the lack of coordination, have clearly affected our under-

standing of the distribution and roles of host-associated microbes. For example, a recent

microbiome comparison of several Indo-Pacific invertebrate species demonstrated that

sponges have a less specific microbiome than had been assumed for many years [35]. Expand-

ing the taxonomic breadth of host–microbe studies will be most fruitful in areas where taxo-

nomically rigorous field guides, ecological survey data, and functional trait databases are

available. Substantial progress will also occur where phylogenetic relationships are known and

local expert taxonomists can be engaged. One of the numerous potential outcomes includes

building community-wide association matrices to unveil the extent of reliance between hosts

and microbial partners (specificity versus ubiquity, obligate versus facultative) and the interac-

tions that promote the stability of core microbiomes.

Role of microbes in host acclimatization and adaptation

Host-associated microbes can rapidly respond to extrinsic factors such as extreme or anoma-

lous environmental conditions (e.g., heatwaves, hypoxia), pathogens, anthropogenic distur-

bances (e.g., pollution, overfishing, aquaculture, invasive species), and acute and chronic

stressors [36,37]. They can also quickly change in response to factors intrinsic to the host (e.g.,

changes in host physiology [38]). The dynamic nature of microbes may provide a source of

ecological and evolutionary novelty to support potential host response mechanisms that aug-

ment the host’s own evolutionary potential. Host-associated microbial communities can shift

rapidly through the loss, gain, or replacement of individual members. Individual microbial

cells can make rapid physiological adjustments during their lifetime (plasticity) or within a few

generations (adaptation) [39] (Fig 2). In many microbes, relatively high rates of mutation and

exchange of genetic material among divergent lineages (through homologous recombination

and horizontal gene transfer) generate a high frequency of new genetic variants, some of

which may be better suited to novel conditions (Fig 2). These mechanisms contribute to fuel-

ing an immense standing pool of genetic variation that hosts can potentially draw upon. The

outcomes of the collective ecological and evolutionary response of hosts and their associated

microbes to environmental change may comprise 1 of 4 nonmutually exclusive scenarios

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[40,41]: (1) Imbalance: a temporary or permanent change of host fitness and microbial func-

tions leading to increased disease susceptibility; (2) Resistance: the microbiome continues per-

forming its functions and the host does not lose or gain fitness; (3) Acclimatization: the newly

formed microbial community in conjunction with host phenotypic plasticity enable the indi-

vidual host to adjust and maintain performance under changing environmental conditions

(Fig 2); and (4) Adaptation: in the long term, newly formed interactions between host geno-

types and associated microbes increase the fitness of the symbiosis and th

Resource

Deep-Learning Resources for Studying Glycan-

Mediated Host-Microbe Interactions

Graphical Abstract

Highlights

d Glycan-focused language models can be used for sequence-

to-function models

d Information in glycans predicts immunogenicity,

pathogenicity, and taxonomic origin

d Glycan alignments shed light into bacterial virulence

Bojar et al., 2021, Cell Host & Microbe 29, 132–144
January 13, 2021 ª 2020 The Author(s). Published by Elsevier In
https://doi.org/10.1016/j.chom.2020.10.004

Authors

Daniel Bojar, Rani K. Powers,

Diogo M. Camacho, James J. Collins

Correspondence
diogo.camacho@wyss.harvard.edu
(D.M.C.),
jimjc@mit.edu (J.J.C.)

In Brief

Bojar et al. present a workflow that

combines machine learning and

bioinformatics techniques to analyze the

prominent role of glycans in host-microbe

interactions. The herein developed

glycan-focused language models and

alignments allow for the prediction and

analysis of glycan immunogenicity,

association with pathogenicity, and

taxonomic classification.

c.
ll

OPEN ACCESS

ll

Resource

Deep-Learning Resources for Studying
Glycan-Mediated Host-Microbe Interactions
Daniel Bojar,1,2 Rani K. Powers,1,2 Diogo M. Camacho,1,4,* and James J. Collins1,2,3,4,5,*
1Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
2Department of Biological Engineering and Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge,

MA 02139, USA
3Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
4These authors contributed equally
5Lead Contact

*Correspondence: diogo.camacho@wyss.harvard.edu (D.M.C.), jimjc@mit.edu (J.J.C.)

https://doi.org/10.1016/j.chom.2020.10.004

SUMMARY

Glycans, the most diverse biopolymer, are shaped by evolutionary pressures stemming from host-microbe
interactions. Here, we present machine learning and bioinformatics methods to leverage the evolutionary in-
formation present in glycans to gain insights into how pathogens and commensals interact with hosts. By
using techniques from natural language processing, we develop deep-learning models for glycans that are
trained on a curated dataset of 19,299 unique glycans and can be used to study and predict glycan functions.
We show that these models can be utilized to predict glycan immunogenicity and the pathogenicity of bac-
terial strains, as well as investigate glycan-mediated immune evasion via molecular mimicry. We also develop
glycan-alignment methods and use these to analyze virulence-determining glycan motifs in the capsular
polysaccharides of bacterial pathogens. These resources enable one to identify and study glycan motifs
involved in immunogenicity, pathogenicity, molecular mimicry, and immune evasion, expanding our under-
standing of host-microbe interactions.

INTRODUCTION

In contrast to RNA and proteins, whose sequences can be eluci-

dated from their associated DNA sequence, glycans are the only

biopolymer outside the rules of the central dogma of molecular

biology. Although glycans are synthesized by DNA-encoded en-

zymes (Lairson et al., 2008), an individual glycan sequence is

dependent on the interplay between multiple enzymes and

cellular conditions. Additionally, the expansive glycan alphabet

of hundreds of different monosaccharides allows for a large

number of potential oligosaccharides, built with different mono-

saccharides, lengths, connectivity, and branching. Glycans are

present as modifications on all other biopolymers (Varki, 2017),

exerting varying effects on biomolecules, including stabilization