Information

10.0: Introduction - Biology


A human, as well as every sexually reproducing organism, begins life as a fertilized egg (embryo) or zygote. Trillions of cell divisions subsequently occur in a controlled manner to produce a complex, multicellular human. In other words, that original single cell is the ancestor of every other cell in the body. Once a being is fully grown, cell reproduction is still necessary to repair or regenerate tissues. For example, new blood and skin cells are constantly being produced. All multicellular organisms use cell division for growth and the maintenance and repair of cells and tissues. Cell division is tightly regulated, and the occasional failure of regulation can have life-threatening consequences. Single-celled organisms use cell division as their method of reproduction.


17.0 Introduction

Figure 17.01 – A Child Catches a Falling Leaf: Hormones of the endocrine system coordinate and control growth, metabolism, temperature regulation, the stress response, reproduction, and many other functions. (credit: “seenthroughmylense”/flickr.com)

Chapter Objectives

After studying this chapter, you will be able to:

  • Identify the contributions of the endocrine system to homeostasis
  • Discuss the chemical composition of hormones and the mechanisms of hormone action
  • Summarize the site of production, regulation, and effects of the hormones of the pituitary, thyroid, parathyroid, adrenal, and pineal glands
  • Discuss the hormonal regulation of the reproductive system
  • Explain the role of the pancreatic endocrine cells in the regulation of blood glucose
  • Identify the hormones released by the heart, kidneys, and other organs with secondary endocrine functions
  • Discuss several common diseases associated with endocrine system dysfunction
  • Discuss the embryonic development of, and the effects of aging on, the endocrine system

You may never have thought of it this way, but when you send a text message to two friends to meet you at the dining hall at six, you’re sending digital signals that (you hope) will affect their behavior—even though they are some distance away. Similarly, certain cells send chemical signals to other cells in the body that influence their behavior. This long-distance intercellular communication, coordination, and control is critical for homeostasis, and it is the fundamental function of the endocrine system.


  • Title: Microbiology: An Introduction, 12th edition - Required
  • Author: Tortora, Funke, and Case
  • Publisher: Benjamin Cummings
  • ISBN: 978-0-321-92915-2
  • The lab manual is electronic and can be printed from the course Blackboard webpage.
  • Title: A Photographic Atlas for the Microbiology Laboratory, 3rd edition - Recommended
  • Author: Michael Leboffe & Burton Pierce
  • Publisher: Morton
  • ISBN: 0-89582-656-9
  • Title: Microbiology: An Introduction Study Guide - Recommended
  • Author: Tortora, Funke, & Case
  • Publisher: Benjamin Cummings
  • ISBN: 0-8053-7809-X
  • Title: Basic Laboratory Methods for Biotechnology, 2nd edition
  • Author: Lisa A. Seidman and Cynthia J. Moore
  • Publisher: Pearson
  • ISBN: 0321570146

Results

Experimental validation for single-cell analysis in female gametic cells

A tetraploid cell has twice the amount of DNA relative to a diploid cell, but transcriptome studies have found a small number of genes showing expression changes between tetraploids and diploids in Arabidopsis [19, 20]. This is likely caused by measuring relative gene expression levels that cannot accurately measure transcriptome abundance between polyploid and diploid cells [21]. For example, if the total RNA amount doubles in the tetraploid cell relative to the diploid, the absolute number of gene transcripts would exhibit averagely twofold increase in the tetraploid relative to the diploid (Fig. 1a), whereas the relative expression level of the gene per transcriptome would be identical between diploid and tetraploid cells. In addition, some normalization methods such as spike-in RNA or genomic DNA [18, 23, 33] measure the expression level of each gene to the control (such as spike-in RNA or genomic DNA/ploidy), but not the absolute transcript numbers per gene per cell (Additional file 1: Fig. S1).

Schematic diagram of scRNA-seq analysis in diploid and tetraploid plants. a Relative expression level per transcriptome and absolute transcript number per cell for a gene (red) in a diploid and a tetraploid cell. b Pipeline of scRNA-seq analysis. Each color indicates one type of unique molecular identifiers (UMIs). ERCC, External RNA Controls Consortium. The absolute transcript level per gene is determined by the number of distinct UMIs aligned to each transcript, excluding PCR duplets, which is 2 for gene X, 3 for gene Y, and 2 for one ERCC RNA

To solve this problem, we employed the scRNA-seq approach to quantify the genome-wide changes in absolute transcript levels per gene per cell in diploid and tetraploid plants (Fig. 1b). The choice of cell types is critical for the scRNA analysis. Many plant cell types often undergo endoreduplication [22], which can confound the polyploid (WGD) effect. After evaluating suitable cell types, we selected reproductive (female gametophytic) cells for the study to minimize confounding variables, and these cells are relatively uniform in a given stage. Flowering plants have three distinct female gametic cells, namely, egg, central, and synergid cells. Each egg or synergid cell is a haploid, whereas the central cell is a diploid (2 copies of the maternal genome). We generated two cell-specific lines that each expresses green fluorescent protein (GFP) in the diploid or isogenic tetraploid A. thaliana (Col-0) using the same construct as previously reported [34, 35]. Specifically, pDD45:nGFP and pSUP16:nGFP are expressed in the egg and central cell nuclei, respectively [34]. The synergid-cell GFP line was available only in the diploid plants and used for diploid comparison but excluded from the diploid-tetraploid analysis.

Using the nGFP marker, we manually isolated each egg cell from an ovule of flowers (stage 12) under an inverted dissecting microscope (the “Methods” section). We named the egg cell in the diploid (ECd) and tetraploid (ECt) plants (Fig. 2a). Similarly, the central cells (CCs) from the diploid and tetraploid plants are designated CCd and CCt, respectively (Fig. 2b). The egg and central cells in the tetraploid plants were

1.6-fold (by volume) larger than the corresponding cells in their corresponding diploids (Fig. 2c, d), which is consistent with the cell size increase in yeast polyploids [17] and in stomatal cells of A. thaliana ploidy series [16]. Note that CCs are noticeably larger than the ECs in the same ovule probably because each CC is a diploid (two copies of the maternal genome) in a diploid plant or tetraploid in a tetraploid plant, while each EC is a haploid and diploid in the diploid and tetraploid plants, respectively.

Egg and central cell size changes in diploid and tetraploid plants. a, b Representative images of egg cell (EC) (a) and central cell (CC) (b) isolated from the diploid (upper panel) and tetraploid (lower panel) A. thaliana (Col-0). Scale bar = 30 μm. The GFP-labeled nucleus is shown in green. Nuclear (c) and cell (d) size estimates of EC and CC with different ploidy levels using 5 cells for each cell type as in (a) and (b)

For egg cell and central cell in the diploid and tetraploid plants, scRNA-seq libraries were constructed using eight cells (eight biological replicates) for each cell type as previously described [26, 36] (the “Methods” section). In addition, synergid cells in the diploid plants with four biological replicates were used for scRNA-seq library construction and analysis. An equal amount of External RNA Controls Consortium (ERCC) RNA molecules was added to each cell (Fig. 1b). During reverse transcription, each cDNA molecule was ligated with a unique molecular identifier (UMI) containing 6-bp random sequence (HNNNNN) at the 5′ end, which could be used to correct PCR-induced amplification bias, while the ligation efficiency was estimated using the external RNA controls. The raw transcript number per gene was calculated as the number of distinct UMIs aligned to the gene model, excluding duplicate counts.

Another quality control showed that the majority of sequencing reads were aligned to the transcription start sites of both endogenous genes and ERCC RNAs, indicating good preservation of mRNA integrity during RNA manipulation (Additional file 1: Fig. S2). For the expression of ERCC RNAs, the dependence of the squared coefficients of variation (CV 2 ) on the molecule counts fits the Poisson distribution, which is consistent with previous single-cell RNA-seq studies [25, 37] (Additional file 1: Fig. S3). Moreover, patterns of the female gamete specifically expressed genes (6 in egg cell and 12 in central cell) from the published datasets [38,39,40,41] were reproduced in our scRNA-seq datasets (Additional file 1: Fig. S4), indicating a good reproducibility of cell-specific transcriptomes.

By counting the raw transcript number of observed UMIs, we detected

25,000 transcripts per egg cell and

230,000 transcripts per central cell (Additional file 2: Table S1). Based on the abundance of all ERCC spike-in controls, we found that the capture efficiency of mRNA in scRNA-seq libraries varied from

7%. To eliminate the effect of capture efficiency variation and more importantly to compare expression abundance among different cell types, we normalized average transcript abundance of each gene per egg or central cell using the capture efficiency (the “Methods” section). As expected, the dependence of observed molecule counts (Molobs) on expected molecule counts (Molexp) has fitted a Poisson generalized linear model [log2 (Molobs) = β0 + β1log2 (Molexp)] [42] (Additional file 1: Fig. S5). Thus, the capture efficiency and cell-to-cell technical noise were estimated using Poisson generalized linear regression of all ERCC spike-in controls for each cell (the “Methods” section). For example, the above raw numbers were normalized as average transcript abundance of

6,924,840 per central cell. These normalized values were used for further analysis.

To confirm the reproducibility, we made additional RNA-seq libraries using an artificial mix of two or three egg cells in each library, each with five biological replicates. As expected, normalized numbers of total mRNA transcripts displayed a linear relationship with cell numbers per library (from

449,836 per one egg cell to

1,507,362 per three cells), in spite of some variation among replicates in the two-cell sample (Fig. 3a). The correlation between the expression levels and cell numbers was further analyzed by pairwise comparison of mRNA transcript number levels among the libraries containing different numbers of cells (Additional file 1: Fig. S6a, b). Linear regression analysis showed two and three cells per library had a 1.93-fold and 3.25-fold increase of transcript numbers, respectively, compared with one cell per library highly expressed genes showed a better correlation between transcript abundance and cell numbers than poorly expressed genes. Despite relatively low power for single-cell analysis to detect genes that are expressed at low levels, this result validated a suitability of using scRNA-seq analysis for testing transcriptome changes between different cell types of diploid and tetraploid plants.

scRNA-seq analysis in egg and central cells in diploid and tetraploid plants. a A linear relationship between the total number (k = thousand) of normalized transcripts and the number of cells per library. Black dots indicate mean values with standard deviations of the total number of normalized mRNA transcripts estimated from 8 replicates for 1 cell and 5 replicates each for 2 and 3 cells. b Principal component analysis (PCA) of scRNA-seq data. ECd and ECt: egg cells in diploid and tetraploid plants, respectively CCd and CCt: central cells in diploid and tetraploid plants, respectively. c, d Kernel density estimates of expression fold changes in the egg cells of tetraploid (ECt) and diploid (ECd) plants (c) and in the central cells of tetraploid (CCt) and diploid (CCd) plants (d)

Transcriptome increase in the egg and central cells in tetraploid plants

Pearson’s correlation coefficients of scRNA-seq results among eight biological replicates were > 0.9 for egg cells and > 0.8 for central cells (Additional file 1: Fig. S6c), indicating low transcript number variation within the same type of female gametophytic cells. Principal component analysis (PCA) further separated the expression groups of all transcripts between cell types (egg and central cells) and between ploidy samples (diploid and tetraploid plants) (Fig. 3b). These results provided another valuable assessment of the quality and reproducibility of our scRNA-seq datasets (Additional file 2: Table S1).

For egg cells, normalized mRNA transcripts per cell were

449,836 in the diploid plant (Additional file 1: Fig. S7a, b), which were doubled (

909,969) in the tetraploid plant (P = 0.0001, Monte Carlo simulation, N = 10,000), indicating that genome duplication has a doubling effect on the transcriptome abundance in the egg cell. Consistent with the doubling effect, the peak of fold changes in the kernel density estimation was 1.9 between ECt and ECd (Fig. 3c). However, the central cell of the tetraploid plant showed

1.6-fold increase of the normalized transcript abundance (11,156,304) compared with that (6,924,840) in the diploid plant (P = 0.0002, Monte Carlo simulation, N = 10,000) (Additional file 1: Fig. S7c, d) the peak of fold changes was

1.5 (Fig. 3d). At the genome-wide level, 57% and 58% of the expressed genes (> 3,000) showed larger than 1.5-fold increase after genome duplication in egg and central cells, respectively (Additional file 2: Table S1). The genes with higher expression levels tended to show more ploidy-dependent expression increase than the genes with lower expression levels (Additional file 1: Fig. S7c, d). These results suggest that genome doubling in tetraploid plants can increase overall transcript and gene expression levels, but their fold increases depend on cell types.

Although the central cell has more transcripts than the egg cell, the fold increase of transcriptome changes in the tetraploids is smaller in the former (1.6-fold) than in the latter (2-fold). This could be related to genome-wide demethylation and de-repression of chromatin and/or transcriptional repressors in the central cell. Coincidently, the central cell-specific DNA hypomethylation factor, DEMETER (DME) [43], was expressed 4-fold higher in the tetraploid plant than in the diploid (Fig. 4a). DME activates Polycomb Repressive Complex 2 (PRC2) genes such as fertilization-independent seed 2 (FIS2) [44] and MEDEA (MEA) [45] in the central cell [46]. As a result, expression levels of FIS2 and MEA were increased from 3.8- to 4.3-fold in the tetraploid plant than in the diploid (Fig. 4a). Activation of PRC2 genes can suppress the transcription of many other genes through the induction of histone H3K27 trimethylation (H3K27me3) [47, 48]. Indeed, H3K27me3 target genes identified in a previous study using the endosperm [49] showed significantly lower fold changes than the genes without H3K27me3 in the central cell of tetraploid plants (P < 1e −7 , Wilcoxon rank-sum test) (Fig. 4b). These results suggest that activation of PRC2 genes may contribute to H3K27me3 increase and repression of overall expression levels in the central cell of tetraploid plants. Moreover, increased expression levels of PRC2 genes in the central cell prior to fertilization could help bypass (endosperm) barriers of interspecific hybridization in allopolyploids as previously predicted [50, 51]. Notably, these genes (DME, FIS2, and MEA) are expressed specifically in the central cell and later in the endosperm but not in the egg cell [38] (Additional file 2: Table S1).

Expression validation of PRC2 genes and TOR and OSR2 in diploid and tetraploid plants. a qRT-PCR analysis showing increased expression levels of DME and PRC2 genes (FIS2 and MEA) in the central cells of tetraploid relative to diploid plants. b Relative expression ratio changes of the genes associated with (+) H3K27me3 (H3K27me3 target genes) or without (−) H3K27me3 (H3K27me3 non-target genes) in the central cell between tetraploid (CCt) and diploid (CCd) plants. The ratios were calculated using average expression values from eight biological replicates. The genes associated with H3K27me3 had significantly lower expression ratio changes than the genes without H3K27me3 (P < 1e −7 , Wilcoxon rank-sum test). c, d qRT-PCR analysis showing increased expression levels of TOR (c) and OSR2 (d) in egg and central cells of diploid and tetraploid plants. ERCC_171 was used as an internal control, which was equally added for each cell before reverse transcription. Double asterisks indicate a statistical significance level of P < 0.01 (Student’s t test)

Among the upregulated genes by genome doubling, expression changes of 1,344 and 1,978 genes had larger than a 2-fold increase (P < 0.05, one-way ANOVA) in egg and central cells, respectively (Additional file 3: Table S2). Gene Ontology (GO) analysis showed enrichment of these genes in transcription- and translation-related processes, including translational initiation, mRNA processing, and protein folding (Additional file 1: Fig. S8). The larger size of the egg and central cells in the tetraploid than in the diploid led us to examine whether regulators of cell expansion were also upregulated after genome duplication. Arabidopsis has several key factors involved in cell expansion and size, including ARGOS-LIKE (ARL) [52], TARGET OF RAPAMYCIN (TOR) [53], THESEUS1 (THE1) [54], and ORGAN SIZE RELATED 2 (OSR2) [55]. ARL and THE1 showed very low or no expression in the egg and central cells of diploid plants (Additional file 2: Table S1). Interestingly, expression levels of OSR2 and TOR in the egg and central cells were increased twofold or more in the tetraploid plants relative to the diploid ones (Additional file 2: Table S1) the result was further validated by qRT-PCR (Fig. 4c, d). These data suggest that the cell size regulators may also contribute to cell size increase in response to a ploidy increase.

Consistent with the increased cell size by ploidy, the central cell (diploid) is larger than the egg cell (haploid) from the same diploid plant, albeit of their different cell types (Fig. 2). The central cell had 6,924,840 normalized mRNA transcripts, 15-fold higher than the egg cell in the same diploid plant (Additional file 1: Fig. S7a, c). In addition, the synergid cell in the diploid plant had

2.9 million normalized mRNA transcripts. This suggests that the synergid cell contains more transcripts than the egg cell but less than the central cell, which is consistent with the published observation that the synergid cell is larger than the egg cell but smaller than the central cell [56]. These results suggest a positive correlation between RNA content and cell size [57]. The disproportionally larger than twofold increase in the transcriptome abundance among cell types probably reflects different activities in cell types central cells are more metabolically active than the egg cells [58].

Cell-specific gene expression in egg, central, and synergid cells in diploid plants

Previous studies have generated transcriptome data using micro-dissected female gametophytes or sporocyteless mutant in Arabidopsis [59], wheat [60], rice [61], and maize [62]. In Arabidopsis, laser capture microdissection (LCM) combined with microarray or RNA-seq was commonly used to study gene expression changes in female gametophytic cells [63,64,65], which could result in datasets with mRNA cross-contamination among different cell types [66]. The quality of our scRNA-seq data was tested in the egg cell, central cell, and synergid cell (Fig. 5a). For comparative analysis, both scRNA-seq (this study) and published LCM-RNA-seq [64, 65] datasets were normalized by transcripts per million (TPM) (the “Methods” section). As expected, a subset of known gamete-specifically expressed genes (AT2G21740, AT1G74480, and AT2G21750 in EC AT5G38330, AT3G10890, AT4G25530, AT5G04560, and AT3G04540 in CC and AT1G47470, AT5G43510, AT4G18770, AT5G42955, AT4G07515, AT1G52970, AT2G21655, and AT5G12380 in SC) as reported [34, 41], also exhibited cell-specific expression patterns in our scRNA-seq datasets (Fig. 5a, upper panel). However, expression patterns of these genes were mixed among cell types in the LCM-RNA-seq datasets (Fig. 5a, upper right panel). The scRNA-seq datatsets were largely contamination free, whereas LCM datasets included some seed coat genes (AT1G61720, AT5G48100, AT5G35550, AT4G09960, and AT5G17220) with low expression levels in female gametes.

Gene expression patterns in the female gametes revealed by scRNA-seq analysis. a Clustering analysis of female gamete-expressed genes in LCM datasets [64, 65] and in scRNA-seq data (this study) (upper panel) and new sets of female gamete-expressed genes (lower panel) identified by scRNA-seq analysis. Gene expression levels in scRNA-seq were mean transcript per million (TPM) values of the genes in all cells for each cell type. EC, egg cell CC, central cell SC, synergid cell. b Venn diagram showing the numbers of the genes that are expressed in three female gametophytic cells. An expressed gene is defined as its expression in one or more cells examined. c Expression clustering of all CRP (cysteine-rich peptides) genes in EC, CC, and SC. d Fractions of CPR transcripts out of total mRNA transcripts in EC, CC, and SC

In scRNA-seq datasets, we identified 5,456, 14,619, and 5,460 genes that were expressed (read count > 0 in any of the libraries) in the egg, central, and synergid cells, respectively (Fig. 5b). A total of 12,738 genes (39% of all expressed genes) showed significantly different expression patterns in at least two of the three (egg, central, and synergid) cell types (P < 0.05, one-way ANOVA), indicating enormous expression variation among female gametes. Compared to the egg and synergid cells, the central cell had 2.7-fold more expressed genes, suggesting higher metabolic and biological activities in the central cell (Fig. 5b). Among those genes expressed in cell types, 288, 505, and 7,155 were exclusively expressed in the egg cell, synergid cell, and central cell, respectively (Fig. 5b), including top 20 genes with the highest expression values that are uniquely expressed in each cell type (Fig. 5a, lower left panel). The genes with expression patterns shared among cell types include 2,453 in all three cell types, 2,612 in EC and CC, 103 in EC and SC, and 2,399 in CC and SC (Fig. 5b). GO enrichment analysis of the female gamete-expressed genes indicated that some biological processes are shared among three female cell types, while others are specific to each cell type: embryo development in the egg cell, photosynthesis and response to cytokinins in the central cell, and pollen germination and small GTPase-mediated signal transduction in the synergid cell (Additional file 1: Fig. S9). These results are consistent with respective biological roles in three cell types: embryo development in the egg cell, photosynthesis and energy metabolism in the central cell (progenitor of the endosperm), and assisting pollen tube growth and fertilization in the synergid cell.

Remarkably, a group of gene family members encoding cysteine-rich peptides (CRPs) [67], accounted for a large amount of total normalized mRNA transcripts in the egg (15%), central (21%), and synergid (46%) cells (Fig. 5c, d). CRPs regulate plant growth and development through modulation of cell-cell communications, including the guidance of pollen tube and gamete recognition during fertilization [58, 68]. Among these CRP genes (Additional file 4: Table S3), we randomly selected four newly defined genes (two expressed in the synergid cell and two expressed in the central cell) for functional validation by expressing promoter::GFP in the transgenic lines (Fig. 6). Consistent with the scRNA-seq data, two genes (AT5G48953 and AT3G48231) were expressed in the central cell (Fig. 6a, b), according to the image evaluation methods as previously described [34], while the other two (AT4G35165 and AT3G30247) were expressed in the synergid cell (Fig. 6c, d). The data suggest roles of these cell-specifically expressed genes in female-male gametic interactions between synergid cell and pollen tube (sperm) for pollen guidance and between central cell and sperm in double fertilization for endosperm development.

Validation of expression patterns of CRP genes in promoter::GFP transgenic lines. Expression of AT3G48231 (a) and AT5G48953 (b) in the central cell. AT3G48231 (low-molecular-weight cystine-rich 48): LCR48 AT5G48953: LCR86. Expression of AT4G35165 (c) and AT3G30247 (d) in the synergid cell. AT4G35165, a CRP-encoded egg cell-secreted-like protein AT3G30247, a CRP encoding an ECA1 (early culture abundant 1) gametogenesis-related family protein


CLASSROOM STUDIES

We have given the final version of CLASS-Bio to students in both introductory and upper-division biology courses across four institutions (CU UBC Western Washington University, Bellingham, WA and University of Maryland, College Park, MD). Data from CU's Department of Integrative Physiology (IPHY), MCDB, and EBIO, and UBC's biology program are presented here.

Figure 2A shows the overall pre- and postinstruction percent-favorable scores (percent agreement with experts) in introductory biology courses in two CU departments (EBIO and MCDB) and one UBC program (biology). (Courses are coded A–F for anonymity.) In five of these six introductory courses, there is a significant decrease in the student-matched percent-favorable score across the instruction period (course averages of the paired student data between pre- and postinstruction are considered significantly different if they differ by more than 2 SEM Adams et al., 2006). In other words, students become more novice-like in their beliefs during their introductory biology courses. Examples of individual category shifts from two introductory courses are displayed in Figure 3, A and C.

Figure 2. Overall pre- and postinstruction percent-favorable scores (percent agreeing with expert) in introductory (A) and upper-division (B) courses. Courses are coded by course (letter), instructor (number), and year. Introductory courses are represented by two CU departments (EBIO and MCDB) and one UBC department (biology) while upper-division courses are represented by two CU departments (MCDB and IPHY). Sample sizes are as follows: A1(08), n = 370 A1(09), n = 336 A2(08), n = 287 A2(09), n = 265 C, n = 170 D, n = 504 E1, n = 126 E2, n = 130 E3, n = 126 F(09), n = 81 F(10), n = 79. Asterisks indicate significant differences between pre- and postinstruction scores based on paired student data (>2 SEM).

Figure 3. Pre- and postinstruction scores for CLASS-Bio categories in two example curricula with the introductory course of the series and an upper-division course. For all categories in both curricula (A–B and C–D), preinstruction scores in upper-division courses are either comparable to or, in most cases, higher than either entering or exiting scores in each curriculum's introductory course. While data in both curricula series represent different pools of students between courses (i.e., data do not follow individuals through the curriculum), data across different semesters show consistent patterns of student thinking (see Figure 2). Asterisks denote significant shifts between pre- and postinstruction scores on paired student data within a given category (>2 SEM).

In contrast, student CLASS-Bio overall percent-favorable scores in five upper-division courses in two CU departments show no overall shifts across the instruction period (Figure 2B). This trend holds true when the statements are divided into categories (Figure 3, B and D). Furthermore, in one upper-division course, there were significant expert-like shifts in specific categories at the end of the instruction period (Figure 3B).

Finally, students entering upper-division courses have comparable or higher preinstruction scores than students’ postinstruction scores in introductory courses (examples of two curriculum series are shown in Figure 3, A–B and C–D).


Biology Course Listing

Please visit the Academic Timetable to see which courses are presently being offered and in which location(s). Not all courses listed below run every term or in all locations. For specific details about program requirements and degree regulations, please refer to the Academic Calendar.

An examination of the biological principles underlying questions concerning biodiversity and evolution. Begins with a discussion of biodiversity and the implications of its loss. This is followed by consideration of the evolution of life on earth, exploring the underlying processes of natural selection and ecological interactions. Prerequisite: 4U Biology or its equivalent or permission of the department.

Designed to explore the role of selected cellular and physiological systems in the maintenance of homeostasis in animals under varying environmental conditions, as well as the molecular basis of hereditary and environmental variation. Prerequisite: 4U Biology or its equivalent. Excludes BIOM 1000H.

Designed to provide a basic understanding of the structure of the human body using a systems approach. In order to gain an appreciation of the complexity of the human body, it is examined on both a microscopic and macroscopic level. Prerequisite: 4U Biology and Chemistry. Recommended: 4U Kinesiology.

Designed to provide a basic understanding of the function of the human body using a systems approach. A central theme is the mechanisms used to maintain homeostasis under normal, healthy conditions. Prerequisite: 4U Biology and Chemistry. Recommended: 4U Kinesiology, BIOL 1050H.

The application of basic physical concepts to biological systems. Topics include forces and motion, energy and metabolism, thermodynamics, and fluid dynamics. Recommended: 4U Math. Not for credit toward a major or minor in Physics.

Provides experience in asking and answering questions in biology, exploring the power of the scientific method, and the importance of critical analysis. Examples involve a wide diversity of organisms and approaches, involving the use of a variety of statistical tools. Prerequisite: 60% or higher in BIOL 1020H or 1030H or BIOM 1000H.

Develops a basic understanding of genetics. Mendelian inheritance, chromosome structure, genetic recombination, mutation, the structure of DNA, the nature of genes, and current topics in genetics are investigated using examples from plants, animals, insects, bacteria, fungi, and viruses. Prerequisite: 60% or higher in BIOL 1030H or BIOM 1000H, and 60% or higher in one of BIOL 1020H or 1050H.

An introduction to cell structure and function, including the organization, physiology, architecture, and interactions of cells. Cellular mechanisms of differentiation, development, cancer, and the immune response are explored. Prerequisite: 60% or higher in BIOL 1030H or BIOM 1000H. Recommended: CHEM 1000H and 1010H.

Cross-listed: GEOG-2080H, ERSC-2080H

An introduction to the diversity of invertebrate animals, emphasizing their evolutionary relationships and functional, behavioural, and ecological aspects of their biology. An emphasis is also placed on field techniques of collection and identification of various invertebrate groups. Prerequisite: 60% or higher in BIOL 1020H or 1030H or BIOM 1000H.

An introduction to the diversity of vertebrate animals, emphasizing their evolutionary relationships and functional, behavioural, and ecological aspects of their biology. Required dissections. Prerequisite: 60% or higher in BIOL 1020H or 1030H or BIOM 1000H.

Through didactic classroom lecturing, hands-on laboratories, use of models, and computer-based software examples, students take a regional approach to examine the anatomy and neural control of the musculoskeletal system. Special emphasis is on learning how the various regional structures contribute (both individually and synergistically) toward producing movement patterns. Prerequisite: 60% or higher in BIOL 1051H. Open only to students in the Kinesiology program.

An examination of the interactions between organisms and their environment at the levels of the population, community, and ecosystem. Covers basic concepts, theories, and methods used in ecology and the application of these to ecological and environmental problems. Prerequisite: 60% or higher in BIOL 1020H.

Concepts of exercise physiology with an emphasis on the biochemical, circulatory, respiratory and musculoskeletal adaptations to both acute and chronic bouts of physical activity and exercise and its relation. Special attention is put upon the application of the physiological principles of conditioning for health promotion in an aging population. Prerequisite: 60% or higher in BIOL 1051H. Open only to students in the Kinesiology program.

An examination of the importance of plants in society. Topics include an in-depth look at the role of plants in human population growth, biotechnology, food safety, medicines, and commercial products. Prerequisite: 60% or higher in BIOL 1020H.

Introduces key molecules and concepts in biochemistry. Topics include the properties of water, the thermodynamics of biological systems, and the behaviour of biomolecules in water. Focuses on each of the four major classes of biomolecules-proteins, nucleic acids, carbohydrates, and lipids-as they apply to biological systems. Prerequisite: CHEM 1000H and 1010H.

An exploration of the scientific basis and ecology of agriculture. Abiotic and biotic factors influencing crop productivity, species interactions, energetics, nutrient cycling, cropping systems management and landscape diversity are considered. Traditional, conventional, and intense systems are reviewed in the context of sustainability. Prerequisite: BIOL 1020H or both ERSC 1010H and 1020H. Recommended: SAFS 1001H, BIOL 1030H. Excludes ERSC-SAFS 3350H.

Cross-listed: ERSC-2350H, SAFS-2350H

A study of the pattern of the evolution of life over the past billion years focusing on key events and transitions, and the underlying processes that made them happen. Prerequisite: 60% or higher in BIOL 2050H.

The science behind environmental issues that are primarily biological in nature, including biodiversity, habitat loss, invasive species, and toxicity. Intended for prospective educators, natural area interpreters, and environmental communicators. Prerequisite: 5.0 university credits. Not for credit toward a major or minor in Biology. Excludes ERSC-BIOL 2700Y.

Cross-listed: ERSC-2701H, EDUC-2701H

The science behind environmental issues that are primarily physical or chemical in nature, including energy conservation, global warming, and air and water pollution. Intended for prospective educators, nature interpreters, and others interested in working with the public on environmental stewardship and sustainability initiatives. Prerequisite: 5.0 university credits ERSC-BIOL 2701H highly recommended. Not for credit toward a major or minor in Biology. Excludes ERSC-BIOL 2700Y.

Cross-listed: ERSC-2702H, EDUC-2702H

Examines the theoretical foundations and techniques of DNA analysis with leading-edge technology in light of forensic cases. Students learn the theory and practice of generating forensic DNA evidence. Prerequisite: FRSC-BIOL 2050H, FRSC-BIOL 3700H, BIOL 3080H.

A study of the four basic animal tissue types and how these tissues are subsequently organized into organ systems. An important emphasis is the relation of tissue form to function. Prerequisite: 7.5 university credits and 60% or higher in BIOL 2070H or permission of instructor.

A study of the ecology of freshwater ecosystems, biology, geochemistry, and physics of freshwater lakes, rivers, and streams. Field trips. Prerequisite:: 7.5 university credits including 60% or higher in BIOL-ERSC 2260H, or permission of instructor. Recommended: CHEM 1000H and 1010H.

Explores the ecological properties of rivers and streams. Theoretical concepts of river function are used as foundations for developing knowledge of aquatic communities. Also considers problems in conservation and management of river and stream ecosystems, and addresses how ecological principles are applied to these problems. Prerequisite: Prerequisite: 7.5 university credits including 60% or higher in BIOL-ERSC 2260H, or permission of instructor. Recommended: CHEM 1000H and 1010H.

Fundamental concepts in molecular biology with emphasis on the exploration of structure, function, and cellular synthesis of DNA and RNA. Techniques in recombinant DNA technology as well as their applications in biomedical, forensic, and pharmaceutical research are discussed. Basic techniques in molecular biology and scientific calculations are also introduced. Prerequisite: Prerequisite: 7.5 university credits including 60% or higher in BIOL 2050H and a pass in both CHEM 1000H and 1010H.

An introduction to the organization and diversity of insects. Lectures emphasize insect physiology, ecology, and behaviour. An insect collecting kit for making required insect collection will be available for cash deposit from the Biology Department in April preceding the beginnning of the course. Prerequisite: 7.5 university credits including 60% or higher in BIOL 1020H and 60% or higher in one of BIOL 1030H or BIOM 1000H, or permission of instructor.

The biology of fishes with emphasis on biotic and abiotic factors that affect their life histories, distribution, population dynamics, feeding, and growth. Field work. Prerequisite: 7.5 university credits including 60% or higher in BIOL-ERSC 2260H, or permission of instructor. Strongly recommended: MATH 1051H, MATH 1052H, BIOL-ERSC-GEOG 2080H.

Ancient biomolecules (proteins, lipids, DNA), the conditions under which they preserve, how they are isolated and analyzed. Topics include stable isotopes, ancient DNA, proteomics, and organic residue analysis. Labs provide students with hands-on experience with techniques commonly used in archaeological science (emphasis on bone chemistry). Prerequisite: ANTH 2150H, or 2.5 ANTH credits and three of BIOL 1020H, BIOL 1030H, CHEM 1000H, GEOG 1040H, or PHYS 1001H.

Cross-listed: ANTH-3153H, FRSC-3153H

Examines major transitions in the evolution of terrestrial plants with a focus on the evolutionary relationships among the main lineages of the flowering plants and the mechanisms underlying the tremendous diversity of this group. Prerequisite: 7.5 university credits including 60% or higher in BIOL 2600H, or permission of instructor.

Due to a sessile nature, plant functioning is unique and highly dynamic. Emphasizing the flowering plants, this course provides an introduction to plant anatomy, physiology, and molecular biology. It examines the mechanisms by which plants work and survive in their role as energy providers to the biosphere. Prerequisite: 7.5 university credits including 60% or higher in BIOL 1020H and at least 1.0 BIOL credit at the 2000 level, or permission of instructor. Strongly recommended: BIOL 3170H. Excludes BIOL-SAFS 3530H.

An intensive coverage of the central nervous system, its anatomy, and physiological interactions. Emphasizes subcortical and cortical brain structures and their functional characteristics. Prerequisite: 8.0 university credits including a pass in PSYC 2200H or 60% or higher in one of BIOL 2070H, 2110H, 2130H, or 3840H.

An examination of the relationship between brain function and psychological processes, drawing heavily from contemporary research involving humans and animals and describing the neural bases for such psychological processes as learning, memory, language, and emotion. Special attention is given to behavioural abnormalities resulting from brain pathology. Prerequisite: 8.0 university credits including PSYC 2200H or PSYC-BIOL 3210H.

Looks at how integrated pest management methods (IPM) are applied to agricultural insect pests. Students will examine the principles of IPM, the role of insects in soil ecology, insects as allies in pest management and as pollinators, monitoring and sampling, and control methods (pesticide and organic). Prerequisite: 7.5 university credits including BIOL 1020H or permission of instructor. Excludes SAFS-BIOL 3110H.

An introduction to microbiology with consideration given to the diversity of microscopic forms, their presence in various habitats, and their impact on humanity. Heavy emphasis is placed on laboratory work. Prerequisite: 7.5 university credits including 60% or higher in BIOL 2070H, or permission of instructor.

Exploration of the scientific basis and practical need for biomonitoring frames the field application of biomonitoring protocols for community clients in terrestrial and aquatic environments. Prerequisite: ERSC 2240H or 2230H or equivalent or ERSC-BIOL 2260H.

The structure and function or proteins, key protein biophysical methods, and enzyme mechanisms are treated in detail. Students use web-based resources such as ExPASy and the Protein Data Bank, and gain practical laboratory experience in bioseparations and the determination of enzyme rate parameters. Prerequisite: CHEM-BIOL 2300H, and one of CHEM-2100H or 2110H.

The key topics are biological processes that produce and use high-energy biomolecules. These include membrane transport, multienzyme pathways, and their regulation. With their skills acquired in CHEM-BIOL 3310H, students are given more freedom for independent laboratory work in devising and executing their own enzyme purification scheme. Prerequisite: CHEM-BIOL 3310H. Excludes CHEM-BIOL 3300H.

Many insect species associated with the process of decay of corpses and their maggots have been used as an important tool for identifying both the timing and location of death. This course explores the relationship between insects and the decay of corpses. Prerequisite: 7.5 university credits including 60% or higher in BIOL 1030H or BIOM 1000H and 1.0 BIOL credit at the 2000 level, or permission of instructor.

An introduction to the biology of amphibians and reptiles. Includes an overview of past and current diversity, the use of amphibians and reptiles as model organisms for biological research, the importance of these animals in ecological communities, and issues in conservation and management. Prerequisite: 7.5 university credits of which 2.0 must be BIOL credits including 60% or higher in BIOL 2260H.

An introduction to the ecological, physiological, and evolutionary mechanisms which influence the behaviour of animals, with particular emphasis on kin selection and co-evolution. Prerequisite: 7.5 university credits including 60% or higher in each of BIOL-ERSC 2260H and BIOL 2600H, and at least one additional 0.5 BIOL credit at the 2000 level or permission of instructor.

Focuses on farming methods and requirements for organic production. The importance of ecological processes, biodiversity, rotation, and organic amendments in organic crop production will be discussed. The standards, certification, packaging, and diversity of markets for organic foods will be emphasized. Mandatory field trips to organic farms. Field trip fee: 30. Prerequisite: SAFS 1001H (2001H) and ERSC-SAFS 2350H.

Cross-listed: SAFS-3370H, ERSC-3370H

Examines current theoretical and applied problems in ecology. Emphasis is placed on developing problemsolving skills, critical evaluation of ecological studies, modelling, and an in-depth look at recent advances in theories and laboratory and field techniques used in solving problems in individual, population, community, and ecosystem ecology. Prerequisite: 7.5 university credits including 60% or higher in BIOL-ERSC 2260H, or permission of instructor.

A lab-based introduction to the anatomy and biology of the human skeleton. Topics include basic skeletal anatomy, bone biology and development, the functional morphology of bones, identification of complete and fragmentary bones, and skeletal pathology. Prerequisite: ANTH 2410H (or 2400Y). Excludes ANTH-BIOL-FRSC 3415Y, 3420H.

Cross-listed: ANTH-3404H, FRSC-3404H

An examination of the prospects for extraterrestrial life, based primarily on material from astronomy, biology, and planetary science. Topics include the origin and evolution of life on Earth, extremophiles, the habitability of Mars and Jovian moons, the nature and habitability of exoplanets, SETI, the Drake equation, and the Fermi paradox. Prerequisite: 5.0 university credits including two of BIOL 1020H, BIOL 1030H, PHYS 1510H, PHYS 1520H. Excludes PHYS 2510H. Not for credit toward a major or minor in Physics.

The mechanisms of plant functioning from the molecular to the whole plant level. Fundamental processes such as photosynthesis, respiration, plant water relations, stomata physiology, mineral nutrition, plant hormone functions, seed germination and dormancy, and environmental stress physiology. Prerequisite: Both SAFS 1001H and 1002H or BIOL 1020H. Excludes BIOL 3180H.

Ecological genetics uses genetic data to investigate ecological and evolutionary processes in natural populations. This course uses theoretical and "real world" approaches to investigate topics that include natural selection and adaptation, behavioural ecology, conservation genetics, invasive species, and phylogeography. Prerequisite: 7.5 university credits including a minimum 60% in each of BIOL-FRSC 2050H, BIOL-ERSC 2260H, and BIOL 2600H. Excludes BIOL-FRSC 3620H, 3700H.

Epidemiology is the systematic study of human diseases and their causes and the application of what is learned to improve health. This course reviews the basic principles and methods of epidemiology, with an emphasis on critical thinking and application to public health and clinical research. Prerequisite: 7.5 university credits including 60% or higher in BIOL 2000H or a pass in NURS 2030H, MATH 2560H, or PSYC 2018H.

Nutrition is the integrative science of what foods our body requires for health, growth, maintenance and reproduction. This course covers the fundamentals of human nutrition, critically assesses evidence underlying dietary claims, and enables students to think critically about the complex interrelationships between food, nutrition, health, and society. Prerequisite: 7.5 university credits including 60% or higher in BIOL 1051H and 2070H.

Introduces students to the application of genetics to the study of taxonomy, structure of natural populations, mating systems, and forensics. Topics include the molecular tools that quantify genetic variation, mathematical models of population structure, paternity analysis, and DNA fingerprinting. Prerequisite: 7.5 university credits including FRSC-BIOL 2050H, or permission of instructor. Excludes FRSC-BIOL 3620H, BIOL 3600H.

The processes of digestion, osmoregulation and excretion, circulatory systems and gaseous exchange, respiration, metabolism, and their control are considered. Uses a comparative approach, first discussing the basic principles of the physiology of these processes and then examining the means whereby different organisms perform them. Prerequisite: 7.5 university credits including 60% or higher in BIOL 2070H and a pass in CHEM 1000H and 1010H, or permission of instructor. Strongly recommended: CHEM 2300H and Animal Care Course.

An examination of fundamental concepts in sensory, endocrine, muscular, and reproductive physiology. Prerequisite: 7.5 university credits including 60% or higher in BIOL 2070H and a pass in CHEM 1000H and 1010H, or permission of instructor.

Students are placed in research projects with community organizations in the Peterborough area. Each placement is supervised jointly by a faculty member and a representative of a community organization. For details see Community-Based Research Program (p. 265). Prerequisite: A minimum cumulative average of 75% and at least 3.0 BIOL credits taught by members of the Trent Biology Department.

Students are placed in research projects with community organizations in the Peterborough area. Each placement is supervised jointly by a faculty member and a representative of a community organization. For details see Community-Based Research Program (p. 265). Prerequisite: A minimum cumulative average of 75% and at least 3.0 BIOL credits taught by members of the Trent Biology Department.

This course provides an opportunity for more intensive or broader study of a selected topic under the guidance of a faculty member. Open to students who have earned at least 3.0 credits in Biology courses taught by members of the Trent Biology department and have achieved a cumulative average of at least 75% in Biology courses completed. Application forms are available from the Biology Office. All University deadlines as specified in the University Calendar apply. These courses may not be taken in the same academic session as BIOL 4900Y, 4901H, 4902H and 4903H.

This course provides an opportunity for more intensive or broader study of a selected topic under the guidance of a faculty member. Open to students who have earned at least 3.0 credits in Biology courses taught by members of the Trent Biology department and have achieved a cumulative average of at least 75% in Biology courses completed. Application forms are available from the Biology Office. All University deadlines as specified in the University Calendar apply. These courses may not be taken in the same academic session as BIOL 4900Y, 4901H, 4902H and 4903H.

This course provides an opportunity for more intensive or broader study of a selected topic under the guidance of a faculty member. Open to students who have earned at least 3.0 credits in Biology courses taught by members of the Trent Biology department and have achieved a cumulative average of at least 75% in Biology courses completed. Application forms are available from the Biology Office. All University deadlines as specified in the University Calendar apply. These courses may not be taken in the same academic session as BIOL 4900Y, 4901H, 4902H and 4903H.

Students investigate a specific field of interest under the guidance of a faculty member. BIOL 4020D is a double credit in Biology. BIOL 4010Y is a single credit because the same thesis is submitted to the other department/program in a joint-major or is submitted in conjunction with BIOL 4400Y. Prerequisite: 15.0 university credits the Animal Care Course (p. 20), if applicable a minimum average of 75% in BIOL courses completed and agreement of a faculty member to supervise the project. (In some cases, it may be possible to take BIOL 4020D with an overall average of 70% in Biology courses if recommended by a faculty member willing to supervise it.) To be accepted into a joint thesis course, the student must meet the requirements of both programs. Applications may be obtained from the department website at trentu.ca/biology/experience.

Students investigate a specific field of interest under the guidance of a faculty member. BIOL 4020D is a double credit in Biology. BIOL 4010Y is a single credit because the same thesis is submitted to the other department/program in a joint-major or is submitted in conjunction with BIOL 4400Y. Prerequisite: 15.0 university credits the Animal Care Course (p. 20), if applicable a minimum average of 75% in BIOL courses completed and agreement of a faculty member to supervise the project. (In some cases, it may be possible to take BIOL 4020D with an overall average of 70% in Biology courses if recommended by a faculty member willing to supervise it.) To be accepted into a joint thesis course, the student must meet the requirements of both programs. Applications may be obtained from the department website at trentu.ca/biology/experience.

Theoretical and practical instruction in design of research projects, with emphasis on appropriate statistical methods through the use of the statistical program R. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including one of MATH 1052H (or 1050Y) or BIOL-GEOG-ERSC 2080H. Excludes GEOG 3030H.

At least 16 hours per week otherwise as CHEM 4030Y. May not be combined with any other project courses for credit toward the Biochemistry & Molecular Biology degree. Prerequisite: An average of 75% in all previous Chemistry courses and permission of instructor.

Examines the chemistry of freshwater systems. Chemical and physical processes that lead to changes in water quality are discussed. The emphasis is on the concentrations and distributions of contaminants. Topics include watershed contributions of chemicals, acidification and the carbonate system, weathering, redox chemistry, trace materials, and synthetic organic contaminants. Prerequisite: ERSC 2230H or ERSC-CHEM 2620H (or 2600Y).

Cross-listed: ERSC-4060H, GEOG-4060H

Discusses approaches to predicting the fate of contaminants in aquatic systems. Basic assumptions and algorithms of fate models for toxic metals and organic xenobiotics are examined and students get hands-on experience in applying recent models to case studies. Prerequisite: ERSC-GEOG-BIOL 4060H.

Cross-listed: ERSC-4070H, GEOG-4070H

An exploration of the cellular and molecular bases of embryonic development. Emphasis is placed on how the intricate and diverse processes of embryogenesis are dependent on common mechanisms, including cell division, cell death, adhesion, migration, gene expression, and intra- and inter-cellular signalling. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL 2070H.

An examination of current concepts of the biology, epidemiology, and evolution of infectious diseases. Topics include emerging disease, the meaning of symptoms, effects of infectious disease on human evolution, Darwinian medicine, vaccines, and virulence. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits.

Focuses on fundamental aspects of human cell biology ranging from organelle function to intercellular communication. Recent technological advances in the field are also discussed. The goal of this course is to develop a holistic view of the cell to enable an understanding of its importance to life and human disease. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL 2050H, 2070H, and 3080H.

An introduction to the study of birds. Covers broad areas in ornithology, including field identification, systematics, ecology, behaviour, anatomy, physiology, management, and conservation. Field trip at cost to student. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including at least 2.0 BIOL credits at the 2000 level.

An introduction to the immune system, including a discussion of the organs, cells, and molecules that constitute, as well as regulate, the immune system. Health-related aspects of the immune system, such as immunodeficiency, tumour immunology, and allergies are also explored. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL 2070H.

An exploration of the evolution, anatomy, ecology, behaviour, and management of terrestrial mammals. Labs are devoted to field techniques and species identification, with emphasis on Canadian forms. One-day field trip at cost to the student. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL 2110H and BIOL-ERSC 2260H.

Examines the physiological and biochemical adaptations to acute and chronic exercise with specific emphasis placed upon the oxygen transport system. The effects of a variety of conditions including age, gender, environmental conditions, and disease on these adaptations are also considered. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL 1051H or 3830H.

Covers classic topics in mathematical biology, including population biology, epidemiology, and mathematical ecology of a single or interacting species. The course addresses modeling of life-science problems by using difference/differential equations and applications of dynamical systems theories. Prerequisite: MATH-PHYS 2150H.

Principles and practices of fisheries assessment and management, including an examination of management problems in freshwater and marine fisheries from ecological, socio-economic, and policy perspectives. Topics include stock assessment techniques, stocking and fertilization, management of warmwater and coldwater species, and local management initiatives. Prerequisite: 10.0 university credits including one of ERSC-BIOL 2260H or ERSC 2210H or 2240H. Recommended: One of ERSC 3510H or BIOL 3050H or 3140H. Students who have successfully completed ERST-CAST 2520H and 2525H may take the course, but must be prepared to do additional background reading.

Examines plant nutrition, soil fertility, and fertilizer management, with a focus on essential macronutrients. Topics include biogeochemical cycling of nitrogen, phosphorus, potassium, calcium, magnesium, and sulphur in crop production. Sustainable management of nutrients for optimum productivity and minimum impact on the environment will be discussed. Prerequisite: GEOG-ERSC-SAFS 3560H.

Cross-listed: SAFS-4270H, ERSC-4270H, GEOG-4270H

The essential biological roles of metals are usually acknowledged but seldom discussed in most biochemistry courses. Includes an introduction to coordination chemistry and a survey of the roles of metals in enzyme catalysis, oxygen transport, photosynthesis, cell mobility, gene expression, and environmental toxicity. Prerequisite: CHEM-BIOL 3310H and 3320H (3300H) or CHEM 2200H and CHEM-BIOL 2300H.

A survey of the questions that are of greatest interest to biochemists. Relies extensively on reading and understanding primary literature sources published within the last four years. Students give presentations in class as part of the course evaluation. Prerequisite: CHEM-BIOL 3310H and 3320H (3300H).

An introduction to human pharmacology divided into two sections: pharmaco-kinetics and pharmacodynamics. Drugs to be studied include mainstream medications such as antibiotics, ethanol, and drugs used in the treatment of pain, high blood pressure, asthma, ulcers, and depression, as well as a brief discussion of alternative medications. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including both CHEM 1000H and 1010H and one of BIOL 3830H or 3840H.

Emphasizes the causes and consequences of global environmental change and their interactions with ecological processes in freshwater ecosystems. Issues such as biodiversity, population growth and water use, global warming, land use, emergent diseases, dams, aquaculture, fisheries, water supply, and sustainability are discussed. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including MATH 1052H (or 1050Y) and one of BIOL 2000H or BIOL-ERSC 2260H. Recommended: GEOG-BIOL-ERSC 2080H.

Biological stoichiometry is the study of balance of energy and multiple chemical elements in living systems including its effects on organismal biochemistry, nutrition, physiology, and ecological dynamics. This course focuses on the principles, application, and recent advances in the field of biological stoichiometry. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including one of BIOL 2070H or BIOL-ERSC 2260H.

Introduces the symptoms of various diseases and the disordered physiological processes that cause these symptoms. Seminars examine specific diseases through discussion of case studies. By the end of the course, students should be able to understand and describe how physiological processes are altered in various common diseased states. Prerequisite: A minimum overall average of 65% in completed BIOL courses 10.0 university credits including BIOL 3830H or BIOL 3840H or BIOL 1051H plus 2.0 BIOL credits at the 2000 level. Excludes BIOL 4350H, 4360H.

Examines the impact of microorganisms on scientific research, the environment, and human health and disease. Particular emphasis is placed on new or emerging areas of microbiology such as microbial ecology, microbial evolution, the human microbiome, and antibiotic resistance. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL 3250H.

An introduction to mechanisms controlling gene expression and applications of recombinant DNA technology. Topics include transcription initiation and post-transcriptional regulation, structure of transcription factors, and specific examples of genetic switches in both prokaryotes and eukaryotes. Seminars include discussion and analysis of journal articles on gene expression research. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL 3080H.

A focus on the causes and consequences of reductions to biodiversity and the strategies to counterbalance these reductions from both their biological and human dimensions. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits. Strongly recommended: BIOL-ERSC 2260H.

An apprenticeship at a collaborating agency working in biological conservation. Students assist in a project pertaining to research and conservation of living things for the equivalent of approximately six hours per week. Evaluation is based on a written appraisal from the agency, as well as a written report and an oral presentation. Open only to Honours students in Biology or Conservation Biology. Prerequisite: 13.5 university credits, a minimum cumulative average of 75%, BIOL 3600H (or 3620H), and BIOL-ERSC 2260H or permission of instructor. Co-requisite: BIOL-ERSC 4390H. Enrolment is limited and competitive. Students must apply in the academic year before enrolment in the course. Application forms may be obtained from the department website at trentu.ca/biology/experience and must be submitted to the placement officer. BIOL 4400Y may be taken jointly with BIOL 4010Y where the project warrants, but the student may not receive credit for a single-credit thesis in another department or program.

Examines human dietary behaviour as a product of interactions among ecology, culture, and biology. It focuses on basic nutritional and ecological principles, diet from evolutionary, comparative, and historical perspectives, cultural factors influencing diet, food as medicine, and the impact of under-nutrition on human physiology and behaviour. Prerequisite: ANTH 2410H (or 2400Y) or permission of instructor.

Cross-listed: ANTH-4440H, SAFS-4440H

Analysis of animal and plant population demography, including theoretical population ecology, population size and survival estimation, patterns and mechanisms in population growth and regulation, multispecies population dynamics, harvesting, and population projection models. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL 3380H.

Examines the quantitative assessment of biological parameters impacting species and populations at risk under governmental species-at-risk legislation. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL-FRSC 2050H or BIOL 2260H.

Examines the biology of animal and plant invasions, focusing on the life history adaptations and dispersal strategies which contribute to their success at both the individual and population levels. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL-ERSC 2260H.

Students gain knowledge of microbes and other biological agents used in criminal endeavours and an overview of the methods used to detect crimes involving biological agents and link them to individual perpetrators. Bioterrorism and agricultural bioterrorism are discussed. Prerequisite: 60% or higher in FRSC 1010H and 1011H and one of BIOL 3080H, FRSC 3000H, FRSC 3111H, or BIOL 3250H.

This seminar-based course introduces students to the application of DNA profiling to forensics, medical genetics, and natural resource management (molecular ecology/conservation genetics). Prerequisite: 10.0 university credits including BIOL-FRSC 3700H (or 3620H).

Explores the processes shaping adaptive evolution and key aspects of organismal fitness, including life spans, sex, and gender. Seminars reinforce lecture material, but also cover additional topics. Two writing assignments provide opportunities for independent study. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL 2600H and BIOL-ERSC 2260H.

Epigenetics is the study of gene functions that are mitotically and/or meiotically heritable, but which do not entail a change in the sequence of DNA. This course reviews these epigenetics mechanisms and discusses how they influence cellular identity, development, predisposition to disease, tumorigenesis, and onset of neurological disorders. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including BIOL 3080H.

Examines the implications of climate change for agriculture, including its impacts on agricultural production, and the role of agriculture as both a producer of greenhouse gases and a potential mitigating agent in climate change. Emphasis is on climate and crop growth simulation modelling and scenarios for mitigation and adaptation. Prerequisite: ERSC-SAFS 2002H or 3002H.

Examines the impact of chronic diseases on mobility, physical activity, and exercise, and how to assess physical function. Also examines the impact of exercise on chronic disease prevention, progression, and treatment ("exercise as medicine"). Students are introduced to clinical research in exercise and chronic disease. Prerequisite: A minimum overall average of 65% in completed BIOL courses 10.0 university credits one of BIOL 1051H, 3830H, or 3840H and one of BIOL 2000H, PSYC 2018H, or PSYC 2019H. BIOL 4190H recommended.

Biological data has grown in size and complexity. Bioinformatics-the application of computer programming to the management and analysis of biological information-is necessary for storing, manipulating, and analyzing large datasets. A tutorial-based computer lab focusing on genome sequence data allows students to learn the basics of computer programming and bioinformatics. Prerequisite: FRSC-BIOL 2050H, 4600H, and one of FRSC-BIOL 3000H or FRSC 3111H.

Explores the interactions between the central nervous and endocrine systems, focusing on the hypothalamic-pituitary-adrenal axis. Examines the control of hormone release, including neurotransmitter modulation and steroid feedback during both homeostatic and stressor-induced states. Also, the interaction among stressors, behaviour, the endocrine system, and disease is considered. Prerequisite: A minimum overall average of 65% in completed BIOL courses and 10.0 university credits including one of BIOL 1051H, BIOL 3840H, or BIOL-PSYC 3210H.

A lab-based course focused on soil organisms and soil biodiversity emphasis on the role of organisms in nutrient cycles and plant growth promotion using a hands-on approach to investigate key soil functions. Approaches for analyzing microbial populations and activities in the environment, including molecular techniques are covered. Prerequisite: One of SAFS 1001H, ERSC 1010H, or BIOL 1020H and 1.0 science credit at the 2000 level or beyond in SAFS, ERSC, CHEM, or BIOL. Excludes SAFS 4840H.


10.0: Introduction - Biology

The speed of light is approximately 300,000,000 meters per second. Working with a large number such as this can quickly become awkward and cumbersome. To simplify matters, we often use scientific notation to represent very large and very small numbers.

Using scientific notation,300,000,000 m/sec can also be written as

3 x 100,000,000

where 8 , the exponent , is the number of zeros.

As you see, the larger or the smaller the number the more beneficial the use of the scientific notation.

Large numbers can be written in scientific notation by moving the decimal point to the left. For example, Avogadro's number is approximately 602,200,000,000,000,000,000,000. Using scientific notation this impressive number is simplified to: 6.022 x 10 23

The decimal point is moved left to just after the first number. That first number must be at least 1, but less than 10. In the example above, the decimal point has been moved back by 23 places. That number is now the positive exponent of the base 10.

Numbers less than 1 can be expressed in scientific notation by moving the decimal point to the right. For example, how would we express 0.0006022?

We still have to follow the rule of scientific notation that the first number must be a least 1, but less than 10. In this instance, the decimal point needs to move forward by 4 digits to the first non-zero number. For every place we move the decimal to the right we decrease the power of ten by one. That number can be written as 6.022 x 10 -4 .

During your studies you will often need to calculate numbers that are expressed in scientific notations. These calculations can be done using the laws of exponents. Here we present a brief introduction to multiplying and dividing numbers expressed using scientific notation.

Multiplying Numbers in Scientific Notation

Suppose we have two numbers in scientific notation,

where a and c are real numbers and b and d are integers. If we want to multiply these
numbers, we need to remember that a is being multiplied by 10 b and c is being
multiplied by 10 d . To express the multiplication we write,


The coefficients (a and c) multiply and the exponents (b and d) sum together
under multiplication to give,


Now, let&rsquos take a look at a more concrete example. Suppose we want to find the
product,


First, we need to multiply the coefficients,

Then, we need to multiply the exponential portions by adding the exponents together,

( 10 7 ) × ( 10 2 ) =10 (7+2) = 10 9 .

Putting this together, we get,

However, under the rules of scientific notation, we are only allowed one digit to
the left of the decimal point. To account for this, we need to move the decimal
point in the answer over one more place to get the final answer,


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Reciprocals and Dividing Numbers in Scientific Notation

The reciprocal of a number is simply 1 divided by that number. So, for example,
the reciprocal of 10 = 10 1 is

1/10 = 0.1 = 10 &minus1 = 1× 10 &minus1 .

Likewise, the reciprocal of 100 = 102 is

1/100 = 0.01 = 10 &minus2 = 1 × 10 &minus2 .

More generally, the reciprocal of a × 10 b given by,


As an example, the reciprocal of

8 x 10 5 is

1/8 × 10 -5 = 0.125× 10 -5 = 1.25× 10 -6 .


The rules for dividing numbers in scientific notation are analogous to the rules
for multiplying numbers in scientific notation. That is, the coefficients must be
divided, and the difference of the exponents must be determined. In particular,
if a and c are real numbers and b and d are integers,



Here is a concrete example,


likewise,


***************** TEST YOURSELF - INSERT FLASH WITH RANDOMLY ACCESSED PROBLEMS ****************


This is a very brief introduction to expressing small and large numbers in scientific
notation. This type of notation is important to and convenient for biologists who
typically work on problems that scale over several orders of magnitude.

This is a very brief introduction to important mathematical concepts essential to solving biological problems such as population growth, carbon dating, drug concentrations to name a few of the interesting questions biologists are expected to answer.

You can learn the definitions of exponential and logarithmic functions and their graphical representations and practice what you have learned by applying these concepts to the problems presented to you.

Biomath Tutorials

The Biology Project > Biomath > Introduction to Scientific Notation


$100 credit for Textbook

Reece JB, Urry LA, Cain ML, Wasserman SA, Minorsky PV, Jackson RB. Campbell Biology. 10th Edition. San Francisco, CA: Pearson Benjamin Cummings 2013. ISBN-10: 0-321-775-651

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Continue your studies with Biology 2.

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Contents

  • Preface
  • Acknowledgments
  • Part 1. Principles of development in biology
    • Chapter 1. Developmental biology: The anatomical tradition
      • The Questions of Developmental Biology
      • Anatomical Approaches to Developmental Biology
      • Comparative Embryology
        • Epigenesis and preformation
        • Naming the parts: The primary germ layers and early organs
        • The four principles of Karl Ernst von Baer
        • Fate mapping the embryo
        • Cell migration
        • Embryonic homologies
        • The mathematics of organismal growth
        • The mathematics of patterning
        • The Circle of Life: The Stages of Animal Development
        • The Frog Life Cycle
        • The Evolution of Developmental Patterns in Unicellular Protists
          • Control of developmental morphogenesis: The role of the nucleus
          • Unicellular protists and the origins of sexual reproduction
          • The Volvocaceans
          • Differentiation and Morphogenesis in Dictyostelium: Cell Adhesion
          • Diploblasts
          • Protostomes and deuterostomes
          • Environmental Developmental Biology
            • Environmental sex determination
            • Adaptation of embryos and larvae to their environments
            • Autonomous Specification
            • Conditional specification
            • Syncytial specification
            • Differential cell affinity
            • The thermodynamic model of cell interactions
            • Cadherins and cell adhesion
            • The Embryological Origins of the Gene Theory
              • Nucleus or cytoplasm: Which controls heredity?
              • The split between embryology and genetics
              • Early attempts at developmental genetics
              • Metaplasia
              • Amphibian cloning: The restriction of nuclear potency
              • Amphibian cloning: The pluripotency of somatic cells
              • Cloning mammals
              • Northern blotting
              • In situ hybridization
              • The polymerase chain reaction
              • Transgenic cells and organisms
              • Determining the function of a message: Antisense RNA
              • Differential Gene Transcription
                • Anatomy of the gene: Exons and introns
                • Anatomy of the gene: Promoters and enhancers
                • Transcription factors
                • Silencers
                • Locus control regions in globin genes
                • DNA methylation and gene activity
                • Possible mechanisms by which methylation represses gene transcription
                • Control of early development by nuclear RNA selection
                • Creating families of proteins through differential nRNA splicing
                • Differential mRNA longevity
                • Selective inhibition of mRNA translation
                • Control of RNA expression by cytoplasmic localization
                • Induction and Competence
                  • Cascades of induction: Reciprocal and sequential inductive events
                  • Instructive and permissive interactions
                  • Epithelial-mesenchymal interactions
                  • The fibroblast growth factors
                  • The Hedgehog family
                  • The Wnt family
                  • The TGF-β superfamily
                  • Other paracrine factors
                  • The RTK pathway
                  • The Smad pathway
                  • The JAK-STAT pathway
                  • The Wnt pathway
                  • The Hedgehog pathway
                  • The Notch pathway: Juxtaposed ligands and receptors
                  • The extracellular matrix as a source of critical developmental signals
                  • Direct transmission of signals through gap junctions
                  • Chapter 7. Fertilization: Beginning a new organism
                    • Structure of the Gametes
                      • Sperm
                      • The egg
                      • Sperm attraction: Action at a distance
                      • The acrosomal reaction in sea urchins
                      • Species-specific recognition in sea urchins
                      • Gamete binding and recognition in mammals
                      • Fusion of the egg and sperm plasma membranes
                      • The prevention of polyspermy
                      • Early responses
                      • Late responses
                      • Fusion of genetic material in sea urchins
                      • Fusion of genetic material in mammals
                      • Preparation for cleavage
                      • An Introduction to Early Developmental Processes
                        • Cleavage
                        • Gastrulation
                        • Axis Formation
                        • Cleavage in Sea Urchins
                        • Sea Urchin Gastrulation
                        • Cleavage in Snail Eggs
                        • Gastrulation in Snails
                        • Tunicate Cleavage
                        • Gastrulation in Tunicates
                        • Why C. elegans?
                        • Cleavage and Axis Formation in C. elegans
                        • Gastrulation in C. elegans
                        • Coda
                        • Snapshot Summary: Early Invertebrate Development
                        • Early Drosophila Development
                          • Cleavage
                          • Gastrulation
                          • The Maternal Effect Genes
                          • The Segmentation Genes
                          • The Homeotic Selector Genes
                          • The Morphogenetic Agent for Dorsal-Ventral Polarity
                          • The Translocation of Dorsal Protein
                          • Axes and Organ Primordia: The Cartesian Coordinate Model
                          • Coda
                          • Snapshot Summary: Drosophila Development and Axis Specification
                          • Early Amphibian Development
                            • Cleavage in Amphibians
                            • Amphibian Gastrulation
                            • The Progressive Determination of the Amphibian Axes
                            • Hans Spemann and Hilde Mangold: Primary Embryonic Induction
                            • The Mechanisms of Axis Formation in Amphibians
                            • The Functions of the Organizer
                            • The Regional Specificity of Induction
                            • Snapshot Summary: Early Development and Axis Formation in Amphibians
                            • Early Development in Fish
                              • Cleavage in Fish Eggs
                              • Gastrulation in Fish Embryos
                              • Axis Formation in Fish Embryos
                              • Cleavage in Bird Eggs
                              • Gastrulation of the Avian Embryo
                              • Axis Formation in the Chick Embryo
                              • Cleavage in Mammals
                              • Escape from the Zona Pellucida
                              • Gastrulation in Mammals
                              • Mammalian Anterior-Posterior Axis Formation
                              • The Dorsal-Ventral and Left-Right Axes in Mammals
                              • Snapshot Summary: The Early Development of Vertebrates
                              • Chapter 12. The central nervous system and the epidermis
                                • Formation of the Neural Tube
                                  • Primary neurulation
                                  • Secondary neurulation
                                  • The anterior-posterior axis
                                  • The dorsal-ventral axis
                                  • Spinal chord and medulla organization
                                  • Cerebellar organization
                                  • Cerebral organization
                                  • Adult neural stem cells
                                  • The dynamics of optic development
                                  • Neural retina differentiation
                                  • Lens and cornea differentiation
                                  • The origin of epidermal cells
                                  • Cutaneous appendages
                                  • Patterning of cutaneous appendages
                                  • The Neural Crest
                                    • The Trunk Neural Crest
                                    • The Cranial Neural Crest
                                    • The Cardiac Neural Crest
                                    • The Generation of Neuronal Diversity
                                    • Pattern Generation in the Nervous System
                                    • The Development of Behaviors: Constancy and Plasticity
                                    • Snapshot Summary: Neural Crest Cells and Axonal Specificity
                                    • Paraxial Mesoderm: The Somites and Their Derivatives
                                      • The initiation of somite formation
                                      • Specification and commitment of somitic cell types
                                      • Determining somitic cell fates
                                      • Specification and differentiation by the myogenic bHLH proteins
                                      • Muscle cell fusion
                                      • Intramembranous ossification
                                      • Endochondral ossification
                                      • Osteoclasts
                                      • Progression of kidney types
                                      • Reciprocal interaction of kidney tissues
                                      • The mechanisms of reciprocal induction
                                      • Lateral Plate Mesoderm
                                        • The Heart
                                        • Formation of Blood Vessels
                                        • The Development of Blood Cells
                                        • The Pharynx
                                        • The Digestive Tube and Its Derivatives
                                        • The Respiratory Tube
                                        • The Extraembryonic Membranes
                                        • Snapshot Summary: Lateral Mesoderm and Endoderm
                                        • Formation of the Limb Bud
                                          • Specification of the limb fields: Hox genes and retinoic acid
                                          • Induction of the early limb bud: Fibroblast growth factors
                                          • Specification of forelimb or hindlimb: Tbx4 and Tbx5
                                          • Induction of the apical ectodermal ridge
                                          • The apical ectodermal ridge: The ectodermal component
                                          • The progress zone: The mesodermal component
                                          • Hox genes and the specification of the proximal-distal axis
                                          • The zone of polarizing activity
                                          • Sonic hedgehog defines the ZPA
                                          • Sculpting the autopod
                                          • Forming the joints
                                          • Chromosomal Sex Determination in Mammals
                                            • Primary and secondary sex determination
                                            • The developing gonads
                                            • The mechanisms of mammalian primary sex determination
                                            • Secondary sex determination: Hormonal regulation of the sexual phenotype
                                            • The sexual development pathway
                                            • The sex-lethal gene as the pivot for sex determination
                                            • The transformer genes
                                            • Doublesex: The switch gene of sex determination
                                            • Temperature-dependent sex determination in reptiles
                                            • Location-dependent sex determination in Bonellia and Crepidula
                                            • Metamorphosis: The Hormonal Reactivation of Development
                                              • Amphibian Metamorphosis
                                              • Metamorphosis in Insects
                                              • Epimorphic Regeneration of Salamander Limbs
                                              • Compensatory Regeneration in the Mammalian Liver
                                              • Morphallactic Regeneration in Hydras
                                              • Maximum Life Span and Life Expectancy
                                              • Causes of Aging
                                              • Snapshot Summary: Metamorphosis, Regeneration, and Aging
                                              • Germ Plasm and the Determination of the Primordial Germ Cells
                                                • Germ cell determination in nematodes
                                                • Germ cell determination in insects
                                                • Germ cell determination in amphibians
                                                • Germ cell migration in amphibians
                                                • Germ cell migration in mammals
                                                • Germ cell migration in birds and reptiles
                                                • Germ cell migration in Drosophila
                                                • Spermiogenesis
                                                • Oogenic meiosis
                                                • Maturation of the oocyte in amphibians
                                                • Completion of amphibian meiosis: Progesterone and fertilization
                                                • Gene transcription in oocytes
                                                • Meroistic oogenesis in insects
                                                • Oogenesis in mammals
                                                • Chapter 20. An overview of plant development
                                                  • Plant Life Cycles
                                                  • Gamete Production in Angiosperms
                                                    • Pollen
                                                    • The ovary
                                                    • Experimental studies
                                                    • Embryogenesis
                                                    • Meristems
                                                    • Root development
                                                    • Shoot development
                                                    • Leaf development
                                                    • Environmental Regulation of Normal Development
                                                      • Environmental Cues and Normal Development
                                                      • Predictable Environmental Differences as Cues for Development
                                                      • Phenotypic Plasticity: Polyphenism and Reaction Norms
                                                      • Predator-Induced Defenses
                                                      • Mammalian Immunity as a Predator-Induced Response
                                                      • Learning: An Environmentally Adaptive Nervous System
                                                      • Teratogenic Agents
                                                      • Genetic-Environmental Interactions
                                                      • Coda
                                                      • Snapshot Summary: The Environmental Regulation of Development
                                                      • “Unity of Type” and 𠇌onditions of Existence”
                                                        • Charles Darwin's synthesis
                                                        • E. B. Wilson and F. R. Lillie
                                                        • “Life's splendid drama”
                                                        • The search for the Urbilaterian ancestor
                                                        • Changes in Hox-responsive elements of downstream genes
                                                        • Changes in Hox gene transcription patterns within a body portion
                                                        • Changes in Hox gene expression between body segments
                                                        • Changes in Hox gene number
                                                        • Instructions for forming the central nervous system
                                                        • Limb formation
                                                        • Dissociation: Heterochrony and allometry
                                                        • Duplication and divergence
                                                        • Co-option
                                                        • Correlated progression
                                                        • Coevolution of ligand and receptor
                                                        • Physical constraints
                                                        • Morphogenetic constraints
                                                        • Phyletic constraints

                                                        With a chapter on Plant Development by Susan R Singer, Carleton College

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                                                        10.8 “linear model,”regression model“, or”statistical model"?

                                                        Statistical modeling terminology can be confusing. The (X) variables in a statistical model may be quantitative (continuous or integers) or categorical (names or qualitative amounts) or some mix of the two. Linear models with all quantitative independent variables are often called “regression models.” Linear models with all categorical independent variables are often called “ANOVA models.” Linear models with a mix of quantitative and categorical variables are often called “ANCOVA models” if the focus is on one of the categorical (X) or “regression models” if there tend to be many independent variables.

                                                        This confusion partly results from the history of the development of regression for the analysis of observational data and ANOVA for the analysis of experimental data. The math underneath classical regression (without categorical variables) is the linear model. The math underneath classical ANOVA is the computation of sums of squared deviations from a group mean, or “sums of squares.” The basic output from a regression is a table of coefficients with standard errors. The basic ouput from ANOVA is an ANOVA table, containing the sums of squares along with mean-squares, F-ratios, and p-values. Because of these historical differences in usage, underlying math, and output, many textbooks in biostatistics are organized around regression “vs.” ANOVA, presenting regression as if it is “for” observational studies and ANOVA as if it is “for” experiments.

                                                        It has been recognized for many decades that experiments can be analyzed using the technique of classical regression if the categorical variables are coded as numbers (again, this will be explained later) and that both regression and ANOVA are variations of a more general, linear model. Despite this, the “regression vs. ANOVA” way-of-thinking dominates the teaching of biostatistics.

                                                        To avoid misconceptions that arise from thinking of statistical analysis as “regression vs. ANOVA,” I will use the term “linear model” as the general, umbrella term to cover everything in this book. By linear model, I mean any model that is linear in the parameters, including classical regression models, marginal models, linear mixed models, and generalized linear models. To avoid repetition, I’ll also use “statistical model.”


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