https://genetics.academic.csusb.edu/ 2026-09-06T06:46:42+00:00 https://genetics.academic.csusb.edu/ https://genetics.academic.csusb.edu/_media/wiki:logo.png text/html 2025-01-27T05:15:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/appendix_a?rev=1737954943&do=diff Appendix A. Tetrad analysis in yeast Introduction In Appendix A we will derive a mapping function for bakers' yeast Saccharomyces cerevisiae using a technique called tetrad analysis. A mapping function is a mathematical formula that allows you to calculate map distance between two $A$$B$$A$$B$$a$$b$$A$$a$$B$$b$$a$$b$$A$$B$$A \cdot B$$a \cdot b$$A$$B$$A$$B$$A$$B$$A$$B$$A$$B$$$A; B \times a; b\\ (\text{line 1})$$$A;B$$a;b$$$\frac{A}{a};\frac{B}{B}\\ \text{(line 2)}$$$A$$B$$A$$B$$A; B$$a; b$$A;B… text/html 2025-02-02T04:51:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_01?rev=1738471873&do=diff Table of ContentsStartChapter 02 Chapter 01. Mitosis and meiosis: a primer for genetics Why you should care about meiosis Meiosis is one of the most important and fundamental phenomena in all biology. All understanding of eukaryotic genetics must start with an understanding of meiosis, and all understanding of text/html 2025-01-29T16:32:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_02?rev=1738168328&do=diff Chapter 01Table of ContentsChapter 03 Chapter 02: Defining genes by function What is a gene? Why do we care? Generally speaking, the answer to “what is a gene” has already largely been answered by scientists. Starting from Gregor Mendel's famous pea plant experiments in the 1860s to define the patterns of how observable traits (i.e., RNA $MATα$$MATa$$his3$$HIS3$$his2$$his3$$his3$$CUP1^r$$CUP1^+$$MATα$$MATa$$MATα$$MATa$$MATa$$MATα$$his3$$his3$$his3$$his3$$HIS3$<a id="fig3"></a>$his3$$his3$$his… text/html 2025-02-16T01:52:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_03?rev=1739670751&do=diff Chapter 02Table of ContentsChapter 04 Chapter 03: Defining genes by segregation patterns Introduction The classical definition of a gene is based on Mendel's Laws of Inheritance. Most genetics textbooks teach Mendelian genetics as a matter of course (“because it's how we've ALWAYS done things, duh!$A$$A$$a$$\frac{A}{a}$$A$$a$$A$$\frac{A}{A}$$\frac{A}{a}$$a$$\frac{A}{a}$$\frac{a}{a}$$A$$a$$\frac{a}{a}$$\frac{A}{A}$$\frac{A}{a}$$\frac{A}{A}$$\frac{A}{a}$$A$$shibire$$shibire$$shi$$\frac{shi^-}{sh… text/html 2024-09-02T06:28:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_04?rev=1725258524&do=diff Chapter 03Table of ContentsChapter 05 Chapter 04. Chromosomes and sex linkage Until now our analysis of genes has focused on defining genes based on phenotypic differences brought about by different alleles or by a direct test of function – the complementation test. In Chapters 4 and 5, our analysis will be concerned with tests of $white$$w$$white$$$ \begin{aligned} P: white\text{ ♂} &\times \text{red eyes ♀ (wildtype)}\\&\downarrow\\F1: \text{all} &\text{ red} \text{ (both ♂ and ♀)}\\ &\downar… text/html 2025-02-19T15:57:18+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_05?rev=1739980638&do=diff Chapter 04Table of ContentsChapter 06 Chapter 05. Defining genes by position Besides providing experimental evidence for chromosome theory as discussed in Chapter 04, Morgan's research group also demonstrated that genes (usually) have fixed positions on chromosomes. When we think about gene position, the term locus (plural: loci, pronounced $white$$X$$crossveinless$$cv$$crossveinless$$cv$$\frac{+}{\rightharpoondown}$$\frac{cv}{\rightharpoondown}$$\frac{w}{\rightharpoondown}$$crossveinless$$whit… text/html 2025-03-22T14:55:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_06?rev=1742655353&do=diff Chapter 05Table of ContentsChapter 07 Chapter 06. The physical nature of the gene In Chapters 01-05, we defined genes conceptually as units of function and inheritance. In this chapter we will start with a new way to define genes: a physical definition of the gene. Conceptually this is the simplest way to define a RNA RNA RNA RNA RNA RNA RNA RNA RNA $\frac{3\times10^9}{23}= 1.3 \times 10^8$$X$RNA $shibire$$shibire$$shibire^+$$shibire^-$$shibire$$shibire$ text/html 2025-03-14T14:29:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_07?rev=1741962598&do=diff Chapter 06Table of ContentsChapter 08 Chapter 07. Analysis of gene sequences Although eukaryotic genes may be generally more interesting to most students, it is useful to first consider bacterial genes. Most eukaryotic molecular biologists use bacteria as tools for various things (e.g., molecular cloning; see Chapter 09), so it’s useful to understand how RNA $p = (\frac{61}{64})^{100} = 8.2 \times 10^{-3}$$$660 \times 1000=6.6 \times 10^5 \text{ g/mol}$$$$\frac{1 \times 10^{-6} \text{ g}}{6.6 \… text/html 2025-03-09T19:05:29+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_08?rev=1741547129&do=diff Chapter 07Table of ContentsChapter 09 Chapter 08. Mutations and suppressors A major goal of genetic analysis is to discover new genes and to understand their function. Geneticists use mutations to perturb gene function as a general strategy to study genes. In many ways it's the same conceptual approach that toddlers use to figure how things work in the world - you break things one at a time and see what happens. $lacZ$$lacZ$$lacZ^+$$lacZ1$$lacZ2$$lacZ^-$$lacZ$$lacZ$$lacY$$lacZ$<a id="screen_sel… text/html 2025-03-19T01:04:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_09?rev=1742346268&do=diff Chapter 08Table of ContentsChapter 10 Chapter 09. Complementation in bacteria In this chapter, we initially touch on some concepts in classical E. coli genetics that may not be of practical interest to all students except future microbiologists, such as F plasmids and Hfr mapping. However, it is useful to learn these concepts because later in the chapter we talk about $lacZ$$lacZ^+$$lacZ^+$$lacZ^-$$lacZ^-$$lacZ^+$$sul^r$$amp^r$$kan^r$$tet^r$$amp^r$$R$$M$$R^- M^+$$amp^r$$amp^r$$(\frac{1}{4})^6$$… text/html 2024-09-02T06:33:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_10?rev=1725258803&do=diff Chapter 09Table of ContentsChapter 11 Chapter 10. Gene regulation in bacteria We are now going to look at ways that genetics can be used to study gene regulation. Up to this point, we have examined gene function as something static and unchanging. But many prokaryotic and eukaryotic genes change their activity depending on the environment cells find themselves in. The question we wish to ask is: how do cells adjust the $lacY$$lacZ$$lacI^–$$lacI^–$$lacI^–$$lacI$$lacI$$lacO$$lacP$$lacP$$lacZ$$lac… text/html 2025-04-08T03:58:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_11?rev=1744084734&do=diff Chapter 10Table of ContentsChapter 12 Chapter 11. Gene circuits and epistasis In Chapter 10, we studied regulatory mechanisms in well-known E. coli operons to see how mutations in different elements of the system would behave in dominance tests and cis/trans tests. We also presented the information in reverse - we told you the answer first, then discussed how $lacO$$lacP$$lacZ^+$$lacO$$lacP$$lacZ$$lacI$$lacZ$$lacI$$lacZ$$A$$A$$A$$B$$A$$B$$A$$B$$A$$A$$B$$A^–; B^–$$B^–$$A^–$$B$$A$$A^-$$B^-$$A^-; … text/html 2025-04-15T13:57:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_12?rev=1744725450&do=diff Chapter 11Table of ContentsChapter 13 Chapter 12. Cloning regulated genes in eukaryotes For the last several chapters we have been looking at how one can study and manipulate prokaryotic genomes and how prokaryotic genes are regulated. In the next several chapters we will be considering eukaryotic genes and genomes and considering how model <a id="genome_compare"></a>RNA $lacZ$$lacZ$$lacZ$$lacZ$$lacZ$$lacO$$lacP$$URA3$$URA3$$tet^R$$URA3$$tet^R$$ura3$$URA3$$lacZ$$lacO$$lacP$$lacO$$lacP$$lacZ$$la… text/html 2025-04-29T18:54:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_13?rev=1745952872&do=diff Chapter 12Table of ContentsChapter 14 Chapter 13. Gene regulation in eukaryotes Introduction In Chapter 12 we considered the structure of genes in eukaryotic organisms and discussed a general strategy for identifying and cloning S. cerevisiae genes that are transcriptionally regulated in response to a change in environment. The ability to regulate $GAL$$GAL4$$gal4$$gal4\text{-}1$$gal4$$gal1$$GAL4$$GAL4^+$$gal4^-$$gal1$$gal7$$gal10$$gal1$$gal1$$gal1$$GAL$$GAL$$lacZ$$GAL1$$GAL1$$gal1$$GAL1$$gal4… text/html 2025-04-29T18:56:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_14?rev=1745952996&do=diff Chapter 13Table of ContentsChapter 15 Chapter 14. Using reverse genetics to study molecules Introduction In this chapter we will see how genetics can be used to dissect molecular structure and function. We have seen one example of how genetics can achieve this in Chapter 13 with the $gal4^{81}$mutant - this mutant taught us something about how Gal80p functions in relation to Gal4p. In this chapter we will look at two further examples of how genetics can teach us about molecular function. In ou… text/html 2025-05-05T02:53:42+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_15?rev=1746413622&do=diff Chapter 14Table of ContentsChapter 16 Chapter 15. Transgenes in multicellular model organisms In the next two chapters we will examine some of the ways in which we can study gene function in higher eukaryotes, using the laboratory mouse Mus musculus as an example. A remarkable number of manipulations have been made to the mouse text/html 2025-05-17T04:53:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_16?rev=1747457595&do=diff Chapter 15Table of ContentsChapter 17 Chapter 16. Gene knockouts in multicellular model organisms Totipotent mouse embryonic stem cells Knocking out mouse genes, or deliberately targeting a specific gene for mutation (as opposed to creating random mutants with a chemical mutagen), is a much more complex process than making $X$$X$$X$$neo^R$$neo^R$$neo^R$$tk^{HSV}$$tk^{HSV}$$tk^{HSV}$$neo^R$$X$$tk^{HSV}$$tk^{HSV}$$tk^{HSV}$$tk^{HSV}$$X$$neo^R$$X$$X$ text/html 2025-05-17T04:52:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_17?rev=1747457558&do=diff Chapter 16Table of ContentsChapter 18 Chapter 17. Newer tools for reverse genetics It is useful to briefly describe some newer technologies for reverse genetics that give researchers a bigger and more advanced toolbox for genetic analysis. Most of these tools are developed for use in mice, but generally they can be adapted to different model genetic organisms with some technical tweaks. $neo^R$$lox$$loxP$$loxP$$loxP$$loxP$$lox$$loxP$$loxP$$loxP$$loxP$$loxP$$neo^R$$loxP$$tk^{HSV}$$neo^R$$neo^R$$… text/html 2024-12-24T12:51:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_18?rev=1735044688&do=diff Chapter 17Table of ContentsChapter 19 Chapter 18. The Hardy-Weinberg equilibrium In earlier chapters, we have been carrying out genetic analysis using controlled crosses where the genotypes are known and we can breed organisms however we want. This approach works well when you are studying a model organism, such as $A/a$$\frac{A}{a}$$A$$a$$A$$f(A)$$a$$f(a)$$$p = f(A)\\ q = f(a)$$$p$$q$$p$$q$$p$$A$$p$$q$$$p + q = 1$$$$f(A/A) + f(A/a) + f(a/a) = 1$$$$p = f(A/A)+\frac{1}{2} f(A/a)\\ q = f(a/a)+\… text/html 2024-09-19T00:52:14+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_19?rev=1726707134&do=diff Chapter 18Table of ContentsChapter 20 Chapter 19. Mutation, allele frequency, and selection In the Chapter 18 we saw that in a population, allele frequency does not change from generation to generation, unless: * Mating is not random; * There are mutations; * There is selection; * There is genetic drift or a bottleneck effect;$A$$a$$$ A \xrightarrow{\mu} a $$$A$$a$$q$$p$$q$$q^2$$q$$q$$S$$1-S$$f(A/A)=p^2$$f(A/a)=2pq$$f(a/a)=q^2$$A/A$$p^2$$p^2$$A/a$$2pq$$2pq$$a/a$$q^2$$q^2(1-S)$$q^2(1-S… text/html 2024-09-15T16:31:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_20?rev=1726417886&do=diff Chapter 19Table of ContentsChapter 21 Chapter 20. Effects of inbreeding In this chapter we will examine how inbreeding between close relatives (also known as consanguineous matings) influences the appearance of autosomal recessive traits. Inbreeding will not make a difference for dominant traits because they need only be inherited from one parent or for X-$F$$A$$A1$$A2$$A3$$A4$$F$$A1/A1$$A2/A2$$A3/A3$$A4/A4$$A1/A1$$A1$$A1$$A1$$A1$$\frac{1}{2}$$A1$$\frac{1}{4}$$A1$$\frac{1}{2}\times\frac{1}{2}=… text/html 2024-09-19T02:47:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_21?rev=1726714027&do=diff Chapter 20Table of ContentsChapter 22 Polymorphisms in human DNA sequences Genomes and human genetics The methods of genetic analysis that you have been learning are applicable to to humans. However, we need to combine these genetic principles with an understanding of the physical realities of the human $white$$yellow$$white$$yellow$$0.5 \times 0.2 = 0.1$$0.1^{13}=10^{-12}$$LCT$$LCT$$LCT$$LCT$$LCT$$LCT$$LCT$$LCT$ text/html 2024-11-26T02:34:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/chapter_22?rev=1732588449&do=diff Chapter 21Table of ContentsChapter 23 Chapter 22. Using statistics to evaluate linkage Earlier we made the case for the importance of statistics in human genetics. But statistics are important for all genetics research. We begin our discussion of statistics in human genetics with a brief return to model organisms first. $shi$$vg$$\frac{shi}{+} \cdot \frac{+}{vg}$$\times \frac{shi}{shi} \cdot \frac{vg}{vg}$$shi$$vg$$shi$$vg$$shi$$vg$$shi$$vg$$shi$$vg$$O$$E$$\frac{(O-E)^2}{E}$$\frac{1}{1+1+1+1}\… text/html 2024-09-02T05:27:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/developers_notes?rev=1725254863&do=diff Style guide Center all tables and images. Image centering is built-in functionality when inserting; tables use the <columns> tag as part of the Columns plugin. Genes and gene symbols should use $\LaTeX$ formatting: e.g., $URA3$ or $unc\text{-117}$. In retrospect this was not a great idea because autolink 4 does not recognize $\LaTeX$ text/html 2024-09-02T06:53:22+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/how_to_use_this_book?rev=1725260002&do=diff How to read this book TNBGGA is meant to be a conceptual overview of the genetics of model organisms. It attempts to be readable without overwhelming the reader with details. At the same time, it strives to be as comprehensively descriptive as possible when it comes to concepts. As such, the reader should approach this text not as a $\LaTeX$ text/html 2024-08-24T16:36:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/licensing?rev=1724517417&do=diff The materials in this book were modified from the MIT OpenCourseWare (OCW) 7.03 Genetics course lecture notes and materials from 2004, by Chris Kaiser, Gerald Fink, Leona Samson, and Michelle Mischke. The work is licensed based on the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) License. Any new artwork not directly copied from the 2004 original MIT notes either has copyright information indicated where used or is copyright Mike Chao (2020, 2023, 202… text/html 2024-09-10T04:24:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/sidebar?rev=1725942277&do=diff TNBGGA Table of contents * What is TNBGGA? * How to use this book Part 1: Classic genetics * Chapter 01: Mitosis and meiosis: a primer for genetics * Chapter 02: Defining genes by function * Chapter 03: Defining genes by segregation patterns * Chapter 04: Chromosomes and sex linkage * Chapter 05: Defining genes by position Part 2: Beginning of the modern synthesis * Chapter 06: Physical nature of the gene * Chapter 07: Analysis of gene sequences * Chapter 08: Mutations a… text/html 2024-09-16T22:32:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/start?rev=1726525951&do=diff What is TNBGGA? If you don't care about any of this stuff, click on any of the links in the Sidebar to the left to get started. The No Bullshit Guide to Genetic Analysis (TNBGGA) was developed from a genetics course taught at California State University San Bernardino in Fall 2020, at the height of the COVID-19 pandemic. The pandemic presented challenges to people of all walks of life. In education, the pandemic highlighted inequities in educational opportunities and access to educational res… text/html 2024-11-26T04:11:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/table_of_contents?rev=1732594313&do=diff TNBGGA Table of Contents What is TNBGGA? How to use this book Part 1: Classic genetics Chapter 01: Mitosis and meiosis: a primer for genetics Chapter 02: Defining genes by function Chapter 03: Defining genes by segregation patterns Chapter 04: Chromosomes and sex linkage Chapter 05: Defining genes by position Part 2: Beginning of the modern synthesis Chapter 06: Physical nature of the gene Chapter 07: Analysis of gene sequences Chapter 08: Mutations and suppressors Chapter 09: Co… text/html 2024-09-03T06:03:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/testpage?rev=1725343391&do=diff This is a test page. Lab Table of Contents sidebar text/html 2024-08-26T21:28:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://genetics.academic.csusb.edu/tools?rev=1724707724&do=diff <https://jgostick.github.io/mml2latex/> MathML to LaTeX converter Test page, test silly things here