Integrative Physiology and its Lab (Fall 2015)
Lecture / recitation course: 11:067:300:01;4cr; index:09914; T1F3 lecture (9:15-10:35AM; 12:35-1:55PM), W1
recitation (9:15-10:35AM); Lab course: 11:067:301:01;1cr; index:09915; W2. (10:55AM – 12:15PM); Both courses are
in Bartlett 123. Dr. JP Advis; (848) 932-9240; e-mail: advis@aesop.rutgers.edu; Office Hours: in Bartlett r102 (MT 11AM
- 2PM and on F 11AM - 12PM), or by appointment; course website: http://rci.rutgers.edu/~advis/
MEETINGS & DATES
TOPICS
TEXTBOOK CHAPTERS
01
02
03
04
05
06
Tue Sept 01 Lecture: The Basis of Animal Function (prerequisites)
Wed
02 Lecture: Membranes - Movement across them (prerequisite)
Wed
02 Lec/Rec/Lab: Homeostasis & Signal Transduction / Intro Rec/Lab #01
Fri
04 Lecture: Endocrine Communication (principles of hormonal systems)
Tue
08 (no classes due to Labor Day scheduling)
Wed
09 Lecture: Neural Communication (mechanisms and sensory systems)
Recitation and Lab #1 on the Basis of Animal Function
Recitation and Lab #2 on Membrane-related and Homeostatic events
Recitation and Lab #3 on Endocrine & Neural Communication,& Muscle
07 Fri
11 Lecture: Muscle contraction and the Control of body movement
08 Tue
15 REVIEW #1 - Material from lectures #1 through lecture #7
09 Wed
16 EXAM #1 - 20% of final grade (lectures #1 through #8)
1-5
1-5
1-6
7
10
11
12
13
14
15
16
17
18
19
20
21
Fri
Tue
Wed
Fri
Tue
Wed
Fri
Oct
Tue
Wed
Fri
Tue
Wed
18
22
23
25
29
30
02
06
07
09
13
14
Lecture: Cardiovascular (CV) Design and the Heart as a Pump
Lecture: Blood Pressure and CV function (in health and disease)
Recitation and Lab #4 on Heart and Blood Pressure related functions
Lecture: CV integration / Basics of Respiratory System Mechanics
Lecture: Gas Transport and Control of Respiration / The renal system
Recitation and Lab#5 on CV Integration and the Respiratory System
Lecture: The Kidney, Clearance and the Countercurrent Mechanism
Lecture: Clearance and the Regulation of Water and Inorganic Ions
Recitation and Lab #6 on the basic functions of the Renal System
Lecture: Gastrointestinal (GI) motility, secretion, digestion and absorption
REVIEW #2 - Material from lecture #12 through lecture #18
EXAM #2 - 20% of final grade (lectures #1 through #18 + #20)
14-16
17
14-17
17-18
18-19
14-18
19
19-20
19-20
21
1-20
1-20
22
23
24
25
26
27
28
29
30
Fri
Tue
Wed
Fri
Tue
Wed
Fri
Tue Nov
Wed
16
20
21
23
27
28
30
03
04
Lecture: Regulation of Organic Metabolism, Growth and Energy Balance 21-23
Lecture: Neuroendocrine Control of Food Intake and Energy Balance
23-25
Recitation and Lab #7 on Metabolism, Food intake and Energy Balance 21-25
Lecture: From Sex Differentiation to Adult Reproduction in males / females 26
Lecture: Neuroendocrine Control of Reproduction & Reproduction Cycles 26
Recitation and Lab #8 on basic physiology of the Reproductive System
26
Lecture: Role of Biological Clocks in Animal Health and Production
1-26
REVIEW #3- Material from lecture #19 through lecture #27
1-26
EXAM #3 - 20% final grade (lectures #1 through #27 + #29)
1-26
31
32
33
34
35
36
37
38
39
Fri
Tue
Wed
Fri
Tue
Wed
Fri
Tue
Wed
06
10
11
13
17
18
20
24
25
Lecture: Stress, Immunity and the Physiology of Health and Production
Lecture: Physiology of Health and Production: Growth and Muscles
Recitation and Lab #9 on Stress and Physiology of Health and Production
Lecture: Physiology of Health and Production: Exercise and Racing
Lecture: Physiology of Health and Production: Ovulation and Lactation
Recitation and Lab #10 on Stress and Physiology of Health & Production
Discussion of lectures #01-09 / Review of test #1 lecture topics
Discussion of lectures #10-30 / Review of test #2 lecture topics
Discussion of lecture #31-36 / Review of test #3 lecture topics (F class)
NO
40 Tue Dec
41 Wed
Fri
42 Tue
43 Wed
8-11
1-5
1-6
1-11
12-13
1-13
1-13
21-23
23-25
21-25
26
26
1-26
1-26
1-26
1- 26
CLASSES – THANKSGIVING RECESS (from Thu Nov 26 to Sun Nov 29)
01
02
04
08
09
Discussion of recitation questions from #01 through #05
1-26
Discussion of recitation questions from #06 through #10
1-26
Deadline for submitting edited final answers of recitation questions
REVIEW #4 - Material from lecture #29 + lectures #31 through #36
1-26
EXAM #4 - 20% final grade (meetings #01 through #41)
1-26
EXAM #5 – 20% of final grade (mean final answers recitation questions)
Textbook: “Human Physiology, 7ed, by Dee Ungleb Silverthorn, Pearson, Benjamin Cummins Publishers
th
(2016). The 6 ed. Of this book (2013) is also acceptable for this course. All students are required to have
access to this text. This book is available at the Cook-Douglass Bookstore and also at the Rutgers Fennen
Mall College Bookstore.
Top Hat: In addition, students have the opportunity to access the Boundless Physiology Text, an electronic
textbook based on “punch-lines” as well as its question’s database. Student cost for a FREE ACCESS of
the Boundless textbook will be $25. If interested, contact TopHat using the following information: Course Name: Fall 2015 Integrative Physiology Direct URL: https://app.tophat.com/e/829319 6-­‐digit course code: 829319
Exams and grades: There are no make-up exams. Student’s problems with exam dates must be discussed with the instructor
BEFORE the exam. If a student fails to do so, and does not show up to take the exam at the appointed time a grade of "F" might
be assigned for the missing test. Students with a medical excuse will receive an essay test to replace their missing test. The letter
and % grade equivalence, for a final 75% class average corrected grade, are: A=91-100%; B+=86-90%; B=81-85%;C+=76-80%;
th
C=71-75%; D=61-70%; F=0-60%. Text: Students should have unlimited access to the following text: Human Physiology, 7 ed., by
th
Dee Ungleb Silverthorn. Published by Pearson / Benjamin Cummins Publishers (2016). The 6 ed. of this book (2013) is also
acceptable. This book is available at the Cook-Douglass Bookstore and at the Rutgers Ferren Mall College Bookstore.
Laboratory: In addition to the lecture / recitation course, students might register for the 1 credit Integrative Physiology Laboratory
course (W2, Bartlett 123) that will also reinforce lecture material and will provide further discussion of the lectures, based on
physiological computer simulations directly related to the lecture material (see below). An overview of this laboratory 1-credit
course is located after the next section (see below).
Finally, since recitation take place on W1 and each laboratory on W2, this allows for two consecutive periods to answer
each of the 100 questions of your EXAMS #1 through #4. Although only one period is required to take each test, this
provides an additional and optional extra time for students to take these tests.
The recitation section of the Lecture Integrative Physiology course
This section of the course meets on W1 (except for Sept 2 when we will have the second lecture, instead). Recitations have been
developed as reinforcement for each week material based on a specific essay question, requiring critical thinking. The average of
all your weekly recitation answers will be your EXAM #5 and will have the same weight (20%) as any of your four other tests.
Students should e-mail the instructor (advis@aesop.rutgers.edu) their first draft of each weekly
recitation question the Monday before each recitation is due. The rationale for this weekly deadline
is for students to be able to participate in the coming recitation discussion. By the following week,
students that met the deadline will receive the instructor comments about their recitation answers.
Only answers submitted by the set deadline for each question (see below) are assured to receive
these comments, which you can use to edit further your answers. All late submissions might receive
comments during regular office hours, based on the time availability of the instructor (remember that
the goal of this exercise is to prepare you for the discussion at each weekly recitation by reviewing
the lecture material, week by week). Late submissions students might also get feedback about their
answers during lectures, recitations and lab meetings. Only final edited answers of the recitation
questions will be graded and their average will be each student grade for EXAM #5. The
deadline for submitting the edited final version of all your answers is Dec 05. Thus, students should
consider EXAM #5 as a written essay test having 10 questions that you answer first in a draft form
once a week and which you can edit based on the instructor comments to your specific answer.
Finally, you can also edit each answer based on the general example presented by the instructor at
the recitation, when each weekly question will be debated. Remember that if you want comments
from the instructor about your specific answer, your weekly e-mail answers must be submitted in the
body of the e-mail (NOT as attachments) with your last name followed by “PHYS recitation XX” in
the subject of the e-mail (XX stands for the recitation #, 01 through 10). The instructor’s comments
will be below your answer preceded by the acronym: “JP.-“. Thus, the main punch-line about the
recitation section is the following:
The average grade of your recitation answers is your exam #5. It has the same weight as
each of your other exams (20%), and is an essay with ten questions (one per week) whose
answers you edit before submitting them for grading on Dec 04. Final recitations must be
submitted in a single e-mail with “PHYS rec. final, last name” in the subject box. Except for
questions #1 and #6 (see below), all recitation answers must have the following outline.
Answers not following this outline (sub-questions a, b, c, d) will get a 20% grade (F).
The four sub-questions to be used in answering most recitation questions are:
a)
Name the structure and the function on which your overall answer will be based? Be as specific
as you can in delimiting the boundaries of your example (the most important part of your answer,
since the following b, c, & d sub-questions are based on your answer to this first sub-question, a).
Please notice that only 1 item is required (in your answer it should be labeled as “a”).
This answer should look like: “a.- My structure (S) is …. and its function (F) is …”. In
same cases a second sentence might be needed.
b)
Why do you think that your structure and your function are related? Support your contention
based on 3 lines of evidence based on the chemistry, physics, anatomy, or physiology involved
in your example. Please notice that 3 items are required (answers should be labeled as
“b1, b2, and b3”). One of this answers might look like: “b1.- If I do this experiment and
measure this variable using this technique, this result will suggest that my S/F is correct”.
Please notice that MY question does not ask you to tell me what happens since this can
be copy from any source, but it asked how do you know that your S/F relationship is true.
c)
Which are the levels of organization involved in your example (c1)? Cite events occurring at its
main level of organization (c2) and indicate how they relate to the whole body level (c3). Please
notice that 3 items are required (thus, answers should be labeled as “c1, c2, and c3”).
These answers should look as follows: “c1.- molecular” or any level of organization
involved in your “a” answer (S/F); “c2.- the first event is; the next even is; the middle
event is; the next event is; the last event is”. Five events distributed equidistant from
each other is a good summary for the story line of the your S/F named in your “a” answer.
Finally, “c3.- at a whole individual level my S/F described in “a” plays this role”.
d)
Which are the main feedback mechanisms involved in your example (cite at least two) (d1)?
Expand on one of them (d2) and name 2 absolute requirment for that feedback to work (d3).
Please notice that 3 items are required (answers should be labeled as “d1, d2, and d3”).
These answers should look as follows: “d1.- an increase in this negative feedback ligand
must decrease this variable under control”. This is how you NAME a negative feedback.
For d1 you need to name two negative feedbacks; “d2.- the first event is; the next even
is; the middle event is; the next event is; the last event is”. Five events distributed
equidistant from each other is a good summary for the most important negative feedback
story line involved as a control of the your S/F named in your “a” answer, that you named
in d1; “d3.- this two components are absolutely necessary for the negative feedback
described in d2 to be operational.
The individual (weekly) recitation questions are as follows:
Question #01: Introduction to this lecture / recitation course (pre-requisite material)
Please remember that your answers for questions #1 and #6 do not follow the structural answer
defined above but they have their own formats. The question for this week is as follows: An “active
learning” process is the best approach to study, physiology. This first recitation uses the first two
lectures to outline and practice an active learning process technique. In your report for recitation #01
provide a list of 5 questions that in your opinion, summarize the prerequisite lecture material (first
two lectures), as well as that provided in the assigned chapters of the course textbook (first five
chapters). Answer each of these five questions using no more than 10 sentences per question. Then
start editing your answer for each question, if it is possible, into a single sentence. Keep in mind that
it is quite difficult to summarize information into a single sentence, since it requires that you
comprehend the material you are studying. Thus, accept that if you are not able to write an answer
initially using less than 10 sentences and then editing this answer into a single sentence, you have
not yet fully understand the topic and keep trying, or ask help from your instructor. It is important you
attempt to master this technique (or a similar one) ASAP. Please remember that the best answer for
each of your 5 questions for this report. are at the most 2 sentences long,
Question #02: Membrane and Homeostasis / related events
The question for this week is as follows: Select a homeostatic event and/or physiological system in
which you can show the importance of structure/function relationship, organization levels, and
feedback control. Your answer must follow the outline shown in the introduction (sub-questions a, b,
c, d, see above). Please notice that in this question you select both the structure and the function on
which your answer will be based. Hint: think on “the circle”.
Question #03: Endocrine and Neural Physiological Communication
The question for this week is as follows: Select a neuroendocrine event in which you can show the
importance of structure/function relationship, organization levels, and feedback control. Your answer
must follow the outline shown in the introduction (sub-questions a, b, c, d, see above). Please notice
that in this question you select both the structure and the function on which your answer will be
based. Important hint for your answer: “what does a neuroendocrine event means” ??. Hint: think
on “the circle”.
Question #04: Heart and Blood Pressure - related functions
The question for this week is as follows: Select four characteristics of cardiocytes not present in
skeletal muscle cells, in which you can show the importance of structure / function relationship,
levels of organization, and feedback control. Your answer must follow the outline shown in the
introduction (sub-questions a, b, c, d, see above). Please notice that in this question both the
structure and the function of the four characteristics on which your answer will be based, were
presented in the heart lecture. Please remember that your answer should be structured as follows:
Characteristic #1 (answers a,b,c,d),; characteristic #2 (answers a,b,c,d); characteristic #3 (answers
a,b,c,d); and characteristic #4 (answers a,b,c,d). Hint: think on “the circle” for each one of these four
characteristics.
Question #05: CV Integration and the Respiratory System
The question for this week is as follows: Select a position on the question “how good an athlete is
the horse”. Do you think the respiratory limitations of this specie (e.g. pulmonary hypertension,
exercise induced pulmonary hemorrhage or EIPH) are expression of physiological compensation for
a fit athlete, or are they manifestation of a system being “run down to the ground in a very stressed
athlete”? Your answer must follow the outline shown in the introduction (sub-questions a, b, c, d, see
above). Please notice that in this question both the structure and the function you are asked to
select must be related to the EIPH syndrome. Hint: think on “the circle”.
Question #06: Basic functions of Renal, CV and Respiratory Systems
The question for this week is as follows: Name the physiological responses and/or the relationships
among buffers, respiratory, circulatory and renal systems involved in the homeostatic control
following a metabolic acidosis. It is an absolute requirement that you answer this question based on
the outline below. Precede each section of your answer with its heading, and make sure you answer
ALL aspects outlined in each section. Hint: for this question you really have to think on “the circle”.
The following are the section headings and their requirements:
a) the example: which are the physiological responses and/or relationships among buffers,
respiratory, circulatory and renal systems on which your answer will be based. Which was the
origin of the metabolic acidosis in your example. Be as specific as you can in delimiting the
boundaries of your example and the level(s) of organization your example will involve.
b) the buffer involvement: how does the buffer system attempt to control the homeostatic
variable (blood pH). Which, how and where is the signal to the buffer system recognized as
input (receptors, afferent loop, and integration center), and how did the output of the integration
center reached their targets (efferent loop, targets). The response this signal elicits is an acute
(fast) or chronic (slow) compensatory mechanism.
c) the respiratory involvement: how does the respiratory system attempt to control the
homeostatic variable (blood pH). Which, how and where is the signal to the respiratory system
recognized as input (receptors, afferent loop, and integration center), and how did the output of
the integration center reached their targets (efferent loop, targets). The response this signal
elicits is an acute (fast) or chronic (slow) compensatory mechanism.
d) the circulatory involvement: how does the circulatory system attempt to control the
homeostatic variable (blood pH). Which, how and where is the signal to the cardiovascular
system recognized as input (receptors, afferent loop, and integration center), and how did the
output of the integration center reached the targets (efferent loop, targets). The response this
signal elicits is an acute (fast) or chronic (slow) compensatory mechanism.
e) the renal involvement: how does the renal system attempt to control the homeostatic variable
(blood pH). Which, how and where is the signal to the renal system recognized as input
(receptors, afferent loop, and integration center), and how did the output of the integration
center reached the targets (efferent loop, targets). The response this signal elicits is an acute
(fast) or chronic (slow) compensatory mechanism.
f)
the integration pathways: how (the sensor, afferent, integrator, efferent, effector and
feedback signals) and in which order (buffers, respiratory, cardiovascular, kidney) were the
physiological systems involved, and recruited to participate in the homeostatic response to a
metabolic acidosis. The most important component of this answer is: Why do you think such
a sequential order in this homeostatic response was achieved? Please notice that this
subquestion does NOT ask you to tell me what is the order, but it asks why that order occurred.
Question #07: Physiology of Metabolism, Food intake AND Energy Balance
The question for this week is as follows: The neuroendocrine control of food intake AND thyroid
function involves neurotransmitters / neuropeptides as inputs and outputs to an integrator located in
the PVN (paraventricular nucleus of the hypothalamus, a main integrator center). From a conceptual
view of cell connectivity and function, describe a possible circuitry consisting of neuronal and
endocrine signals to and from the PVN integrator, operating during a typical Thanksgiving day, an
hypermetabolic AND thermogenic condition. Your answer must follow the outline shown in the
introduction (sub-questions a, b, c, d, see above). Please notice that in this question the structure is
defined as the PVN integrator in relation to food intake AND thyroid involvement. You should define
a function associated to the PVN in relation to this hypermetabolic condition (hint: TRH cell bodies
are located in the PVN). Hint: think on “the circle”. This question is an attempt to make you navigate
through two circles. The answer will be achieved if you are able to transform these two circle into
one. It’s a good exercise and summary.
Question #08: Basic physiology of the Reproductive System
The question for this week is as follows: From a conceptual view of nerve cell connectivity and
function describe a mechanism that would allow for a hypothalamic network of GnRH (or two GnRH
sub-networks e.g. tonic vs. phasic) to synchronize both its tonic (or basal pulsatile gonadotropin
release) and its phasic (or preovulatory surge like release of gonadotropin) operation, as it is
observed during the estrous or menstrual reproductive cycles. Consider how the pulsatile output of
such hypothalamic network might affect gonadotropin release during puberty, reproductive
adulthood and menopause (aging). Your answer must follow the outline shown in the introduction
(sub-questions a, b, c, d, see above). Please notice that in this question the structure is defined as
the GnRH neuronal network (or two GnRH sub-networks e.g. tonic vs. phasic) and you should define
a specific function common to puberty, reproductive adulthood and menopause (aging). Hint: think
on “the circle”.
Question #09: Case Studies on Stress, Growth and Meat Production
The question for this week is as follows: Select an homeostatic event and/or physiological system or
question in which you can show the importance of structure/function relationship, levels of
organization, and feedback control related to the use of Ractopamine, a beta-agonist, as a growth
promoter in both animals and humans. Your answer must follow the outline shown in the introduction
(sub-questions a, b, c, d, see above). Please notice that in this question you should define both a
structure and a function associated to the use of Ractopamine as a growth promoter (remember
which was the main punch-line of the growth and production lecture). Hint: think on “the circle”.
Question #10: Case Studies on Stress, Milk and Egg Production
The question for this week is as follows: Select a homeostatic event and/or physiological system or
question in which you can show the importance of structure / function relationship, levels of
organization, and feedback control related to the toxicity induced by fescue in dairy cows. Your
answer must follow the outline shown in the introduction (sub-questions a, b, c, d, see above).
Please notice that in this question you should define both a structure and a function associated with
the thermogenic effect of fescue toxicity in dairy cows (remember which was the main punch-line of
the stress and production lectures). Hint: think on “the circle”.
Optional Lab section of the Lecture Integrative Physiology course
The integrative physiology laboratory course (1 credit) can only be taken if you are register for
the lecture / recitation of the Integrative Physiology course. This computer simulation – based
course (1-credit) was developed to reinforce the material from the lecture / recitation course (4credits). There is NO additional information in this Lab course that is not already required for the
lecture / recitation course. However, this 1-credit course allows for further discussion of the
recitation question, specifically on how “b” answers of the recitation questions could be
approached. As you will soon learn, this “b” answers are conceptually the most difficult portion of
your recitation answers. From your first recitation you learned that an “active learning technique”
is the best way to study physiology. You also learned from your instructor that writing and editing
is the best way to apply this active learning methodology. The introduction section for each lab
experimental paradigm is an excellent summary of concepts presented in the lecture / recitation
course, and it is what you as a student should try to achieve when summarizing and editing
lecture material. In addition, after you read each lab introduction section you will go through a
multiple-choice mini–test to check yourself how much you understood of the concepts in
question. Experimental results are already in the lab course (see website), will be presented
succinctly in the lecture / recitation course, and will be discussed further in the lab meetings. In
the lab course, after you obtained your lab results and hopefully understood them, a second
multiple-choice mini-test is presented for you to self-check your understanding of experimental
results. Understanding experimental results are of paramount importance to be able to answer
the “b” sections of your recitation questions. Your final grades for the 1-credit Lab course will be
based on your recitation answers (which you have to submit for the lecture / recitation course)
and on a short paragraph description for each lab you did. These short paragraphs are what you
in any case will have to do, to go through the active learning process when studying for the
lecture / recitation course. Thus, there is not additional work you will have to do, beyond what
you should do when studying for the lecture / recitation course. The schedule for the Integrative
Physiology Lab 1-credit course is as follows:
Integrative Physiology Laboratory (Fall 2015)
11:067:301:01;1cr; index:09915; Fall 2014; W2, Bartlett 123 (10:55AM – 12:15PM);
Dr. JP Advis; (732)932-9240; e-mail: advis@aesop.rutgers.edu; office hours in Bartlett r102
(MT 11AM-2PM; F 11AM-12PM) or by appointment; course website:
http://rci.rutgers.edu/~advis/
MEETINGS & DATES
01 Wed Sep
02 Wed
TOPICS
TEXTBOOK CHAPTERS
03 Wed
09 Lecture / recitation / lab #01 introduction meeting
09 Laboratory #01 Introduction: Discussion of a good active learning tool
Laboratory #02 Simulations: Membrane & Homeostasis- related events
Laboratory #03 Simulations: Endocrine and Neural Communication
15 Suggested deadline for having finished labs #01, #02, and #03
1-2
1-3
1-8
1-8
04
05
06
07
23
30
07
13
9
9,11
12,13
9,11-13
Wed
Wed
Wed Oct
Wed
Laboratory #04 Simulations: Heart and Blood Pressure-related functions
Laboratory #05 Simulations: CV Integration and the Respiratory System
Laboratory #06 Simulations: Renal System and CV/Respiration Overview
Suggested deadline for having finished labs #04, #05, and #06
08 Wed
09 Wed
10 Wed Nov
21 Laboratory #07 Discussion: Metabolism, Food Intake & Energy Balance
28 Laboratory #08 Discussion: Physiology of the Reproductive System
03 Suggested deadline for having finished labs #07 and #08
14,15
16
14,15,16
11 Wed
Wed
Fri
Dec
11 Laboratory #09 Case Studies: Stress, Growth and Muscle Production
18 Laboratory #10 Case Studies: Stress, Ovulation and Lactation
04 Absolute deadline to have submitted all lab reports
1-16
1-16
Grades: The final grade for this lab course will be the average of each student’s lab reports from labs #01-#06
(50%), and the average from their reports from labs #07-#10 (50%). The former reports (#1-6) include the
recitation answers and a written paragraph for each required lab (see below). The latter (#7-10) only include the
recitation answers. The recitation answers are the same that you have to submit for the lecture/recitation course
so you do not need to send them for the lab course (I will move them from your lecture/recitation course to your
lab course). Thus, the only item you must submit for the lab course is your single summary paragraphs for each
lab you did.
The letter and % grade equivalence, for a final 75% class average corrected grades, are:
A=91-100%; B+=86-90%; B=81-85%; C+=76-80%; C=71-75%; D=61-70%; F=0-60%. Please notice that the
aim of all reports is to help you study, week by week, the lecture material of the integrative physiology course.
Remember, Integrative Physiology (4 credits) and its Laboratory course (1 credit) are not courses in which you
might study just the week before a test and expect to survive.
Computer simulation option 1: The program PhILS (Physiology Interactive Lab Simulations) will be used. This
program from McGraw-Hill publishers (PhILS version 3.0) will be available in a CD at the Cook-Douglass
bookstore. In addition, the same texts used for the lecture course will be used in the lab course (Human
th
Physiology, 6 ed., by Silverthorn. Published by Pearson / Benjamin Cummins Publishers, 2012). This text is
available at the Cook-Douglass Bookstore and also at the Rutgers Ferren Mall College Bookstore.
Computer simulation option 2: Recently, the last editions of the Silverthorn text (6 and 7 eds) are offered with
a computer simulation disk called PhysioEx 9.0. This disks has comparable exercises than those in the PHILS
program (the previous option 1). Thus, any one of these computer simulations could be used for this course. The
Siverthorn’s text goes with any of these two computer simulation programs.
The specific laboratory computer simulations are as follows:
Laboratory #01: Introduction to this “laboratory and discussion” course
An “active learning” process is the best approach to study physiology. This first lab will introduce the use of an active
learning technique to study physiology. For this we will use the first lecture of the Integrative Physiology course, a
student lecture notes, and the textbook related chapters, to practice an active learning process technique.
In your report for lab #01 provide a list of 5 questions that you believe summarize the first lecture material based on
your lecture notes and the assigned textbook chapters, related to the prerequisite material for the Integrative
Physiology course. In addition, for each of these 5 questions, provide an answer having no more than 10 sentences
(ranked by their relative importance). Finally, try to summarize each of all 5 answers into a single sentence or
“punch-line”. Keep in mind that it is quite difficult to summarize information into a simple sentence, since it requires
that you comprehend the material you are studying. Thus, accept that if you are not able to write an answer for each
of the 5 questions using less than 10 sentences and then summarize all answers into a single sentence, you had not
yet fully understand the topic material and keep trying, or ask for help from your instructor. Keep in mind that there is
not ONE best answer. A best answer is always the one you understand the best. It is important that you attempt to
master this technique (or a similar one) ASAP. What follows are unranked ideas that might have come from a
student lecture notes or from a student notes taken (copied) from a textbook (make sure you are not just copying
sentences from your textbook as you go from questions, to summary paragraphs, to single sentence). Feel free to
merge them with your own notes as starting points for this exercise. Keep in mind that Lab #01 is only the first
attempt to this exercise. Lab #02 is similar in nature to lab #01 but instead you have to select a homeostatic event or
physiological system and goes with your recitation #02. Similarly, in lab and recitation #03 you have to select a
homeostatic event or physiological system having a neuroendocrine communication strategy (that is it must have
both a neuronal and an endocrine pathways as part of its operation. Please think on “the circle”). Your first draft email answers for these three labs are due at 8AM on the Monday of the week these recitations will be discussed in
the lab meeting (see course schedule). During the following week you will receive e-mail comments from the
instructor if your first draft was submitted by the deadline (see above). If your submission is late, you will have to go
the instructor’s office hours for comments to your answers or ask during lectures, Thereafter, you may edit your
answers as many times as you want, before submitting the final version of all your 10 labs to be graded by the end
of the course. Remember that if you want comments from the instructor about your specific answer, your weekly e-mail answers
must be submitted in the body of the e-mail (NOT as attachments) with your last name followed by “PHYS recitation 00” in the
subject of the e-mail. The instructor’s comments will be below your answer preceded by the acronym: “JP.-“. Please notice that the
lab questions are the same recitation questions of the lecture course and have the same deadlines, thus you need only to submit
them once as “recitation” answers. Finally, your lab reports also include same computer simulation reports from PHILS. These are
listed at the end of this file for each of the first six labs (#01 through #06). Please send recitation answers and computer simulation
answers in different e-mails. The computer simulation reports are a “punch-line” paragraph indicating the most important “take
home message” for each computer simulation.
The following are students’ notes about the prerequisite material for this Integrative Physiology course, to be used together with
your own notes of the first two lectures for the course and the 5 first chapters of the Silverthorn’s textbook..
Introduction to physiology
• Physiology is the study of biological functions, which at the highest level include self-organization, using energy
and raw materials from surroundings, maintaining integrity in face of disturbances (homeostasis), and
reproduction. Since they result from evolution, there are two levels of scientific explanation for them: the
mechanistic (or “how it works”), and the evolutionary (“how did it get to be this way?”). Teleological explanations
for physiological processes assume organismal features are useful adaptations. This is often a valid approach, but
because of constraints of evolution, not all features are logical or optimized.
• Physiology is inherently integrative, requiring knowledge of physics, chemistry, genomics and molecular biology,
anatomy, and evolution. Comparative physiology provides broad insights into understanding life’s functions by
studying all types of organisms. The hypothetic-deductive method is the most widely accepted version of “the
scientific method.” It consists of asking questions, making initial discoveries, proposing testable hypotheses,
making predictions from those hypotheses and testing the predictions.
Levels of Organization
• An organism is an interactive society of cells, which are the basic units of both structure and function. Each cell
performs basic functions essential for its own survival, such as obtaining O2 and nutrients, eliminating wastes,
synthesizing needed cell components, reacting to changes in their environment, controlling movement of
materials, and reproducing.
• In multicellular organisms each cell performs additional specialized activities, that contributes to the function of the
whole organism, which are usually an elaboration of basic cell functions. Animal cells are highly organized into
functional groupings, with cells of similar structure and specialized activity organized into tissues. There are four
primary tissues: (1) muscle, specialized for contraction, movement and force generation; (2) nervous, specialized
for initiation and transmission of electrical impulses for rapid communication; (3) epithelial, which lines and covers
body surfaces and cavities and also forms secretory glands; and (4) connective tissue, connects, supports, and
anchors various body parts.
• Tissues are further organized into organs, which are structures composed of several types of primary tissues
acting together to perform one or more functions. Organs make up body systems, which are collections of organs
that perform related functions and interact to accomplish a common activity essential for survival of the whole
body. Organ systems, in turn, compose the whole body.
Homeostasis
• Homeostasis is the maintenance of a dynamic steady state within the ECF in which multicellular organism’s cells
live. Factors that are often homeostatically maintained are (1) concentration of nutrients, (2) concentration of O2
and CO2, (3) concentration of waste products, (4) pH, (5) concentration of water, salt, and electrolytes, and (6)
volume and pressure. Some animals also maintain (7) temperature.
• Most intrinsic and extrinsic control systems operate on the principle of negative feedback: a change in a
regulated variable triggers a response that drives the variable in the opposite direction of an initial change, thus
opposing the change. Often there is a built-in set point that indicates the ideal state. Effector control can be
antagonistic (that, is can correct for disturbances in both directions), and can be behavioral as well as based on
individual internal organs. Inadequacies in basic negative feedback systems can be improved with feedforward or
anticipation systems (which take corrective action before a disturbance occurs) and acclimatization systems
(which improve an existing system response to chronic or long-term change).
• Not all states are homeostatic all of the time. Useful regulated changes (rheostasis) can be simply turned on or
off as needed, or regulated by reset systems (alter the set point of a negative feedback system) or by positive
feedback (which acts to enhance a change once it has started). Pathophysiological states ensue when one or
more of organisms systems fail to function properly so that an optimal internal environment can no longer be
maintained. Serious homeostatic disruption leads to death.
Organization of Regulatory and Organ Systems
• Regulation is hierarchically arranged from cell to organ to whole-animal levels. Cells are able to regulate some of
their own states and processes, without suffering from delays that would occur if they had to await commands
from a distant “higher” integrator. However, higher integrators are needed to coordinate responses of multiple
organs, for needs that often override those of individual cells.
• Control systems are (1) intrinsics (inherent compensatory responses of an organ to a change), and (2) extrinsics
(triggered by factors external to the organ, primarily by nervous and endocrine systems).
• Functions performed by most systems are often directed toward maintaining homeostasis. Each body system’s
functions ultimately depend on the specialized activities of the cells composing the system. Thus, homeostasis is
essential for each cell’s survival, and each cell contributes to homeostasis.
Introduction to cellular structures
• Complex organization and interaction of chemicals within a cell confer the unique characteristics of life. The key
chemicals are water, certain small inorganic solutes such as salts, and four categories of organic molecules:
lipids, carbohydrates, amino acids and proteins, and nucleotides and nucleic acids.
• Large organic complexes and macromolecules—membranes, polysaccharides, proteins, and nucleic acids—are
responsible for the main structures and functions of cells. Functions often require they be flexible and dynamic,
but in turn, they are susceptible to disruption by some environmental factors such as temperature. Thus,
homeostasis in part evolved to protect the macromolecules, especially proteins.
• Cells, the living building blocks of multicellular bodies, consist of: (1) plasma membrane, encloses the cell and
separates intracellular and extracellular fluid; (2) nucleus, contains DNA; and (3) cytoplasm, portion of cell’s
interior not occupied by the nucleus. The cytoplasm consists of cytosol, a complex gelatin-like mass, and
organelles, which are highly organized, membrane-enclosed structures dispersed within the cytosol.
Nucleus, chromosomes and genes
• The eukaryotic nucleus contains DNA in linear strings called chromosomes. The sequence of a particular stretch
of DNA, a gene, has a code for making proteins, and a regulatory sequence for controlling the coding region of the
gene. A gene is transcribed as an mRNA binds to a ribosome, where it is translated into a protein. Different genes
are expressed in different tissues and organs. Special proteins, transc1iption factors, which often differ among
tissues, recognize the regulatory sequence of a gene, and transcription of the nearby coding section of the gene
might ensues. Telomeres protect the ends of chromosomes and are lost at each cell division. When they are
gone, cell division ceases, a stage link to species’ lifespans.
• Genomics analyzes genetic codes and seeks to understand functions and regulations of all genes. New
technologies associated with genomics include: 1) immunofluorescence, using fluorescent antibodies that bind to
proteins in tissues, revealing their locations visually; 2) “knocking out” (removing) a gene to see its effects; 3) DNA
microarrays (“gene chips”), which can detect active and inactive genes in different tissues and under different
conditions; 4) transgenic organisms, in which genes from one species are inserted into another, for the purposes
of researching how genes work, production of useful products, and gene therapy (adding functional genes to an
individual with a malfunctioning gene); 5) cloning of an individual, which involves taking a nucleus from an
advanced cell (e.g., adult skin cell) and inserting it into an activated egg which has had its own nucleus removed.
Organelles
• Compartmentalization of specific sets of chemicals within organelles permits activities that would not be
compatible with each other to occur simultaneously. Six types of organelles are found in most cells: endoplasmic
reticulum (ER), Golgi complex, lysosomes, peroxisomes, mitochondria, and vaults. The ER is a single complex
membranous network enclosing a fluid-filled lumen that synthesize proteins and lipids to be used for (1)
production of new cell components, mainly cell membranes, and (2) secretion of special products such as
enzymes and hormones. RER’s ribosomes synthesize proteins, which are released into the ER lumen so they are
separated from the cytosol. Also entering the lumen are lipids made within the SER. Synthesized products move
from RER to SER, where they are packed and discharged as transport vesicles. Transport vesicles are formed as
a portion of the SER “buds off,” containing a collection of newly synthesized proteins and lipids wrapped in SER
membrane. The Golgi complex is stacks of flattened, membrane-enclosed sacs that: (1) modify newly
synthesized molecules delivered to it in crude form from the ER; and (2) sort, package, and direct molecular traffic.
Lysosomes are membrane-enclosed sacs of hydrolytic enzymes that destroy phagocytized foreign material such
as bacteria, demolish worn-out cell parts to make way for new replacement parts, and eliminate the entire cell if it
is severely damaged or dead. Peroxisomes are small membrane-enclosed sacs containing oxidative enzymes,
specialized for oxidative reactions, including detoxification activities. Mitochondria house enzymes of the citric
acid cycle and electron transport chain, which efficiently convert energy in food molecules to usable energy stored
in ATP (oxidative phosphorylation). They utilize molecular O2 and produce CO2 and water as by-products. In the
absence of O2, cells rely on glycolysis, and other reactions which yield considerably less ATP than oxidative
phosphorylation. These anaerobic processes yield byproducts such as lactic acid. Cells use ATP as energy
source for synthesis of new chemicals, membrane transport, and mechanical work. Vaults, which are shaped like
octagonal barrels, are the same shape and size as nuclear pores. It is speculated they may transport messenger
RNA and/or ribosomal subunits from nucleus to RER.
Cytosol and cytoskeleton
• The cytosol contains enzymes involved in intermediary metabolism and the ribosomal machinery for synthesis of
these enzymes as well as other cytosolic proteins. Furthermore, many cells store unused nutrients within the
cytosol in the form of glycogen granules or fat droplets. Also present in the cytosol are various secretory,
transport, and endocytotic vesicles containing materials that are being moved between various organelles and
between these organelles and the plasma membrane.
• Pervading the cytosol is the cytoskeleton, which serves as the “bone and muscle” of the cell. The three types of
cytoskeletal elements—microtubules, microfilaments, and intermediate filaments—are each composed of different
proteins and perform various roles. Collectively, the cytoskeletal elements give the cell shape and support, enable
it to organize and move its internal structures as needed, and, in some cells, allow movement between the cell
and its environment. The eukaryotic cell is a very crowded environment, particularly because of the cytoskeleton.
Crowding affects diffusion and reaction rates that are still being investigated.
Cell to cell adhesion
• Special cells locally secrete a complex extracellular matrix, which serves as a biological “glue” between cells of
a tissue. It consists of a watery, gel-like substance interspersed with three major types of protein fibers: collagen,
elastin, and fibronectin.
• Many cells are further joined by specialized cell junctions, of which there are three types: desmosomes, tight
junctions, and gap junctions. Desmosomes serve as adhering junctions to hold cells together mechanically and
are especially important in tissues subject to a great deal of stretching. Tight junctions actually fuse cells
together to seal off passage between cells, thereby permitting only regulated passage of materials through the
cells. These impermeable junctions are found in the epithelial sheets that separate compartments with very
different chemical compositions. Gap junctions are communicating junctions between two adjacent but not
touching cells. Cells joined by gap junctions are connected through small tunnels that permit exchange of ions and
small molecules between them. Such movement of ions plays a key role in the spread of electrical activity to
synchronize contraction in heart and smooth muscle.
Laboratory #02: Membrane and Homeostasis - related events
Your report for lab #02 should include the answer for lab simulation #37 plus at least one extra lab simulation from
PHILS related to this lab topic (see list below) with its attached questions (you are welcomed to do as many
additional computer simulations as you want). If you are using the PhysioEx 9.0 computer simulation, just pick
a similar version from that CD instead of the one in this list that is based on the PHILS computer simulation.
List of lab simulations from PhILS v3.0 for lab #02:
Osmosis and diffusion
01 varying ECF concentration
Metabolism
02 size and basal metabolic rate
03 cyanide and electron transfer
Digestion
37 Glucose transport
Laboratory #03: Endocrine and Neural Physiological Communication
Your report for lab #03 should include the answer for lab simulation #13 and at least one other laboratory simulation
from PHILS related to this lab topic (see list below) with its attached questions (you are welcomed to do as many
additional computer simulations as you want). If you are using the PhysioEx 9.0 computer simulation, just pick
a similar version from that CD instead of the one in this list that is based on the PHILS computer simulation.
List of lab simulations from PhILS v3.0 for lab #03:
Resting potential
08 resting potential and external K
09 resting potential and external Na
Action potentials
10 the compound action potential
11 conduction velocity and temperature
12 refractory period
13 measuring ion currents
Synaptic potential
14 facilitation and depression
15 temporal summation of EPSPs
16 spatial summation of EPSPs
Endocrine function
17 thyroid gland and metabolic rate
Skeletal muscle function
04 stimulus dependent force generation
05 the length - tension relationship
06 principles of summation and tetanus
07 EMG and twitch amplitude
Laboratory #04: Heart and Blood Pressure - related functions
Your report for lab #04 should include the answer for lab simulation #21 and at least one other laboratory simulation
from PHILS related to this lab topic (see list below) with its attached questions (you are welcomed to do as many
additional computer simulations as you want). If you are using the PhysioEx 9.0 computer simulation, just pick
a similar version from that CD instead of the one in this list that is based on the PHILS computer simulation.
List of lab simulations from PhILS v3.0 for lab #04:
Frog heart function
18 thermal and chemical effects
19 refractory period of the heart
20 Starling’s law of the heart
21 heart block
ECG and heart function
22 ECG and exercise
23 the meaning of heart sounds
24 ECG and finger pulse
25 electrical axis of the heart
26 ECG and heart block
27 abnormal ECG
Laboratory #05: CV Integration and the Respiratory System
Your report for lab #05 should include the answer for lab simulation #35 and at least one other laboratory simulation
from PHILS related to this lab topic (see list below) with its attached questions (you are welcomed to do as many
additional computer simulations as you want). If you are using the PhysioEx 9.0 computer simulation, just pick
a similar version from that CD instead of the one in this list that is based on the PHILS computer simulation.
List of lab simulations from PhILS v3.0 for lab #05:
Circulation
28 cooling and peripheral blood flow
29 blood pressure and gravity
30 blood pressure and body position
Blood
31 pH and Hb - O2 binding
32 DPG and Hb - O2 binding
Respiration
33 altering body position
34 altering airway volume
35 exercise - induced changes
36 deep breathing and cardiac function
Laboratory #06
Basic functions of Renal System and CV/Resp Overview
Your report for lab #06 should include the answer for lab simulation #35 and at least one other laboratory simulation
from PHILS related to this lab topic (see list below) with its attached questions (you are welcomed to do as many
additional computer simulations as you want).
List of lab simulations from PhILS v3.0 for lab #06 (since this list is the same as the one for the previous lab, make
sure you do not use the same simulation for both labs): If you are using the PhysioEx 9.0 computer simulation,
just pick a similar version from that CD instead of the one in this list that is based on the PHILS computer
simulation.
Circulation
28 cooling and peripheral blood flow
29 blood pressure and gravity
30 blood pressure and body position
Blood
31 pH and Hb - O2 binding
32 DPG and Hb - O2 binding
Respiration
33 altering body position
34 altering airway volume
35 exercise - induced changes
36 deep breathing and cardiac function
Laboratory #07: Physiology of Metabolism, Food intake & Energy Balance
Your report for lab #07 should include only your answer to recitation question #07, since there is no laboratory
simulation neither from PHILS nor from PhysEx 9.0 related to this lab topic.
Laboratory #08: Basic physiology of the Reproductive System
Your report for lab #08 should include only your answer to recitation question #08, since there is no laboratory
simulation neither from PHILS nor from PhysEx 9.0 related to this lab topic.
Laboratory #09: Case Studies on Stress, Growth and Meat Production
Your report for lab #09 should include only your answer to recitation question #09, since there is no laboratory
simulation neither from PHILS nor from PhysEx 9.0 related to this lab topic.
Laboratory #10: Case Studies on Stress, Milk and Egg Production
Your report for lab #10 should include only your answer to recitation question #10, since there is no laboratory
simulation neither from PHILS nor from PhysEx 9.0 related to this lab topic.