This textbook is up-to-date and appears, as it is in a modular form, relatively easy to update. Linkage to online content is always fraught with issues as content appears and disappears, thus some links do not work currently. This is one serious problem for any complex subject. Excessive details and unfamiliar and occasional misleading nomenclature can alway make it hard to grasp.
The online lectures work well to help with this. In many cases the author has done a fine job of explaining some of the unusual terminology that arose as scientists discovered the workings of the cells. However, at times, the author jumps around from subject to subject which can be hard to follow. This is a serious issue with this book. The flow is too jumpy.
I would hope that students taking this class would already have taken a basic chemistry class first. The bright blue links is a bit distracting. I'm not sure the purple challenge boxes help, they seemed distracting to me. The images are often of low resolution and poor quality font rendering when in a diagram or image.
Italics fonts are hardest read when they degrade. Higher resolution images need to be used. I can see that Dr. Bergstrom has meticulously drawn many of these himself, and they are good, just did not translate well. Perhaps image compression in Adobe Acrobat was set too high. Overall, a very good introductory book.
I like the accompanying video lectures. Needs some editing, fact-rehecking, image reacquisition, and reorganization. Dependence on other's potentially transient on-line content is always an issue. But overall a good resource for students in the biological sciences. The text provides coverage of a very broad range of topics, starting with biochemistry, moving into molecular biology, and ending with cell biology. Throughout the entire text evolution is a constant theme, providing context, rationale, and Throughout the entire text evolution is a constant theme, providing context, rationale, and examples of its importance in the biological sciences - a strong advantage and an important one in my opinion.
There are one or two guided exercises for students to complete within the text, demonstrating how to use online resources such as those available for creating and visualizing 3D protein structures. The table of contents at the beginning is very useful in order to quickly identify which topics are of interest, and the links accurately move you to the relevant sections of the text.
There is no glossary or index of content, however there is a collection of links to relevant YouTube videos referenced in the chapters at the end of the textbook.
Each chapter ends with a list of important terms, but the definitions or the context of these terms is not provided. The text takes a biochemistry intensive approach to the topic, spending half the text 8 of 16 chapters discussing basic chemistry, proteins structure, energetics, enzyme kinetics, and major metabolic processes.
While some of these topics go into great detail, others do not. For example, the calculation of free energy is given significant coverage, as is aerobic respiration and the Krebs cycle. While photosynthesis is mentioned, as well as the several types of performed by plants C3, C4, CAM , there is very little information on the Calvin cycle, one of the most important carbon fixation process on the planet in my opinion.
The next five chapters , focus on molecular biology. Specifically, replication, transcription, translation, gene regulation, and recombinant DNA technology. Coverage in this section varies as well. While replication, transcription, and translation are all adequately described, gene regulation focuses primarily on prokaryotic operons.
Although mentioned, there is not a lot of information on transcriptional regulation through chromatin remodeling, transcription factor expression and regulation, or miRNA regulation. Processing of RNA is also a little brief in some areas, particularly in mRNA capping and circularization in eukaryotes which is yet another way gene regulation may occur. The last four chapters of the text , focus on cellular biology with a focus on membranes, the cytoskeleton, and cell division.
While the explanation and biochemistry of membrane structure, permeability, and transport is excellent, there is very little on intracellular trafficking of vesicles though trafficking of proteins to particular compartments is discussed. There is no content relating to standard cell signaling pathways. Basic cell structure and function is addressed in the first chapter of the book.
The textbook is, in general, accurate. Although there may be some outdated terminology archaebacteria as a primary identifier rather than archaea or the absence of alternative names Krebs cycle as the only reference with no mention of citric acid cycle or tri-carboxylic acid cycle , I did not see any serious errors in concepts or mechanisms being presented.
The material presented is accurate and presented from an objective scientific viewpoint. Content is up to date. The majority of the topics are tenets in biochemistry, molecular and cellular biology, and not generally subject to significant changes. There are several examples given to keep material relevant and up-to-date, including a short description of the biochemical ramifications of the Atkins diet and similarly designed low-carbohydrate diets.
Discussion of bacterial cell structure in chapter one includes a brief description of bacterial cytoskeletal elements and internal membrane structures both of which are not present in more dated material.
There are not a lot of cultural references or examples that would become dated quickly, and therefore all the content has a mostly timeless quality. There are many links to external material YouTube videos by the author presenting topics, links to external figures, and links to Wikipedia entries which may become out of date quickly depending on the whims of the institutions that host this content, however, as long as these are kept current they can easily be changed to reflect new URLs.
The book is written in a very clear and concise manner. It is written in a narrative form with a somewhat casual tone which makes it easy to read and easy to follow. Jargon and technical terms are listed at the end of each chapter as vocabulary lists.
Learning objectives are outlined at the beginning of each chapter. The textbook excels in being able to move between different sections. Each chapter is a self-contained topic with subdivisions. This is quite helpful in being able to present or assign certain sections and still having them retain all the logical connections you would want them to without having to read the textbook in its entirety. While chapter 14, membrane function, may be a bit ambitious in the amount of material it covers and could be broken down into several topics, it does form a cohesive unit of knowledge on the fundamental biological processes that a membrane performs.
The textbooks chapters are organized in a very logical fashion, each one building on the other to more and more complicated concepts. There is a clear introduction to the text, though as with many science textbooks, there is no ending or wrap up. There is just an end to content. Internally, each chapter has a clear introduction and outline to major topics and sub-topics that are being addressed.
It is easy to find information when searching for it. I had no problems reading, navigating, opening, or in any other way interfering with my ability to read and interact with the textbook. At worst, they are simple technical errors that do not obstruct the meaning or clarity of the information.
There is no cultural relevance in the sense this phrase is generally used. Any examples that are made have no relation to cultural background as they are explanations of natural phenomenon independent of whether humans are here or not. That said, science is culturally relevant to everyone and the more science people do and are aware of — the better. This book does an excellent job of trying to bring science to people and engage them in material that is difficult but approachable.
This textbook is primarily a biochemistry textbook that has been modified to incorporate cell biology. While trying to cover so many different topics, it is unable to address either molecular biology or cell biology with the normal amount of detail that most textbooks in these fields would have.
As a biochemistry text, this is an excellent way to introduce both molecular and cellular biology. As a textbook for a molecular biology or cellular biology course, it may not meet all the content areas desired. The title may be more accurately changed to reflect this focus. Overall, without looking into details of every chapter, the book seems to cover properly the subject. The main index is ok. The book has a list of key words at the end of each chapter, but no glossary.
The text introduces some techniques to The text introduces some techniques to demonstrate how discoveries in the field were made. The beginning of each chapter contains learning objectives, which is a good feature. At the end of some chapters, it is possible to direct students to quizzes. It allows customization by different instructors which will probably expand the areas covered in the book.
Parts of the text have problems with wording, which brings some inaccuracy and confusion. Saying that proteins are inserted into the membrane is more accurate. Instead, it would be better to introduce the concept of assembly and disassembly of the nuclear envelope, which are highly coordinated events.
As an additional note, despite the fact that the text emphasizes publication as one important aspect of the scientific method, the book does not have any links or references to scientific articles. Instead, it has quotes from Wikipedia, which sometimes might have problems with quality of information. The book probably will have good longevity. In any case, due to its license and the way the book is designed, it should be easy to make modifications and customize content to add updated information.
It is hard to pinpoint the take-home message of each paragraph. Examples and terms sometimes read like a list. I think that students could have trouble distinguishing what is important and what is not so important to know. Poor modularity. The reader will probably be lost with so many subtitles and with big paragraphs densely packed with words.
The text is redundant at times and the sentences tend to be too long. The text is disorganized at times. These examples could probably come after the definition or in a side note. Cellular structures seems to be presented as if they were a list. I can envision students potentially having trouble focusing on the main points and trying to memorize each term without a real understanding or connection to function.
Unlike most of the other books from the Open Textbook Library, the access to the full version of this textbook is not straightforward. The download of complete version requires filling out a form to be granted access. In fact, I never received a notification to allow the download of the complete version. Therefore, this review is mostly based on the sample chapter chapter 1 , which seems to be the complete version of just one chapter.
Most pictures in this textbook have low resolution, look fuzzy and are poorly labeled. Legends are embedded in the text instead of next to the figure. Therefore, it is difficult for the reader to pinpoint details or sometimes even the main purpose of a figure without going back to reread the text and search for the information.
It will likely be more difficult to refer to figures in class, assignments or homework because there are no figure numbers. The text has some grammatical mistakes. I envision that the need of supplying personal information in order to get the complete version of the textbook will hinder access at some level. Overall, the book has nice ideas regarding interactivity, with links to videos, quizzes, notes with questions and mini-assignments.
It is also customizable, which is great. On the other side, if I were to use it for a class, it would require a lot of work to adapt it to my liking because the text is densely packed, difficult to read, somewhat disorganized and the quality of the figures is very poor. A grasp of the logic and practice of science is essential to understand the rest of the world around us.
To that end, the CMB3e iText like earlier editions remains focused on experimental support for what we know about cell and molecular biology, and on showing students the relationship of cell structure and function.
Rather than trying to be a comprehensive reference book, CMB3e selectively details investigative questions, methods and experiments that lead to our understanding of cell biology. This focus is nowhere more obvious than in the chapter learning objectives and in external links to supplementary material. Each video is identified with a descriptive title and video play and QR bar codes. The Learning objectives align with content and ask students to use new knowledge to make connections and deepen their understanding of concept and experiment.
All external links are intended to expand or explain textual content and concepts and to engage student curiosity. Links to full VOP lectures are now at the back of the book. All images in the iText are by the author or are from public domain or Creative Commons CC licensed sources. For all externally sourced images, CC licenses are indicated with the image. A CMB3e Sample Chapter and CMB3e iText for Instructors model additional interactive features, including short 25 Words or Less writing assignments that can be incorporated into almost any course management system, and all of which the author assigned as homework in his flipped, blended course.
These assessments aim to reinforce writing as well as critical thinking skills. My goal in writing this iText is to make the content engaging, free and comparable in accuracy and currency to commercial textbooks.
I encourage instructors to use the interactive features of the iText critical thought questions, YouTube videos, etc. The online iText is the most efficient way to access links and complete online assignments. Nevertheless, you can download, read, study, and access many links with a smart phone or tablet. And you can add your own annotations digitally, or write in the margins of a printout the old-fashioned way!
Your instructor may provide additional instructions for using your iText. His research interests are in the field of molecular biology and evolution as well as in the area of learning technologies in the service of good pedagogy. He has taught required introductory courses and elective course for biology majors as well as advanced and graduate courses. With more than 33 years experience in instruction, he has frequently tested and incorporated pedagogically proven teaching technologies into his courses.
Content Accuracy rating: 5 Coming in at just over pages, the text covers all the basics and throws in a few delights like the origins of life. Clarity rating: 5 Obvious input from students through annotated text makes the text clear and relatable.
Consistency rating: 5 Textbooks like these are usually parceled out with one leading expert coordinating the effort for one or two units.
Modularity rating: 5 The textbook is provided as a pdf to both students and teachers so as to avoid interface issues.
Interface rating: 5 Worries about whether the bookstore has enough copies or students will inadvertently access instructor resources are a thing of the past. Grammatical Errors rating: 5 Bergstrom has obviously read and re-read his own text as it has few if any, grammatical errors. Cultural Relevance rating: 5 No worries taking offense to this text. Comments Kudos to the University of Wisconsin-Milwaukee for recruiting and retaining such a great teacher and to Dr.
Content Accuracy rating: 3 The content of the text appears accurate throughout. Clarity rating: 3 The text is written in a complex manner and diagrams are small and complex and can be hard to decipher, which can make this text less accessible for beginner students.
Consistency rating: 5 The text is internally consistent, using terminology that is consistent throughout and maintaining the same structural design in each chapter. Modularity rating: 5 Each chapter of the text can stand alone well and be rearranged according to the desire of the instructor and college. Interface rating: 2 The biggest issue is that both students and instructors cannot access the text in a normal OER manner where they can read the text directly online without having to contact the author to ask for a copy of it.
Grammatical Errors rating: 5 No grammatical errors were observed in the text. Cultural Relevance rating: 5 The text was not culturally insensitive or offensive and made significant attempts to provide historical context for scientific discoveries by a wide variety of individuals throughout all chapters. Content Accuracy rating: 5 I used this text in the spring of for my senior-level cell and microbiology course.
Clarity rating: 5 I enjoy the way Dr. Bergtrom writes. This text really is a pleasure to read! Consistency rating: 5 Absolutely consistent from one chapter to the next with frequent hyperlinks to both former and future material in each chapter.
Modularity rating: 5 The text is organized in a classic way like other 'big name' cell biology texts. Interface rating: 5 No issues here - Dr. Bergtrom has done a wonderful job! Grammatical Errors rating: 5 Every now and then you might find a mispelled word or a missing punctuation - but you'll have to look hard to find them. Cultural Relevance rating: 5 I believe Dr. Comments I recommend this text highly and without reservation.
Content Accuracy rating: 5 It is accurate and up to date. Clarity rating: 5 The text is easy to read. Consistency rating: 5 Contents and the framework are consistent between the chapters.
Modularity rating: 5 Each chapter begins with an introduction and learning objectives that should help students as well as instructors to focus on the important points to take home. Interface rating: 5 I haven't seen any interface issues with the provided links.
Nothing in biology makes sense except in the light of evolution. Biological systems, of course, follow the rules of chemistry and physics, but biology is a historical science, as the forms and structures of the living world today are the results of billions of years of evolution. Through evolution, all organisms are related in a family tree extending from primitive single-celled organisms that lived in the distant past to the diverse plants, animals, and microorganisms of the present era.
The great insight of Charles Darwin Figure was the principle of natural selection: organisms vary randomly and compete within their environment for resources. Only those that survive and reproduce are able to pass down their genetic traits.
Several notable methods have been developed to identify GRNs from single-cell data 82 , 83 , 84 , and these have been successfully applied to T cell biology, providing novel insights from co-expression analysis data It is worth emphasizing that the detection of regulatory relationships should be possible in a reasonable timescale, as transcriptional changes do not persist forever.
Further, the directionality between genes in identified networks must be validated and refined with perturbation studies or temporal data in order to infer causality. Individual cells are continually undergoing dynamic processes and responding to various environmental stimuli.
Some of these responses are fast, whereas others can be much slower and can occur over the course of many years e. To study genome-scale dynamic processes in bulk cells, the cells must be synchronized using sophisticated techniques In single-cell systems, however, cells are unsynchronized, which enables the capture of different instantaneous time points along an entire trajectory. We can then apply algorithms to reconstruct dynamic cellular trajectories with respect to differentiation or cell cycle progression Table 2.
Maximum parsimony is the basic principle that infers cellular dynamics and has been widely used in phylogenetic tree reconstruction in evolutionary biology 87 , Monocle initially builds graphs in which the nodes represent cells and the edges correspond to each pair of cells.
The edge weights are calculated based on the distance between cells in the matrix obtained from dimensionality reduction using independent component analysis ICA. The minimum spanning tree MST algorithm is then applied to search for the longest backbone. The main limitation of these methods is that the constructed tree is highly complex, and therefore, the user must specify k branches to search.
A more advanced version, Monocle2 89 , has been recently proposed; this version is much faster and more robust than Monocle and incorporates unsupervised data-driven approaches utilizing reversed graph embedding techniques. For cases in which temporal information is available, supervised learning-based approaches can be more accurate. Single-cell clustering using bifurcation analysis SCUBA 90 , for example, implements bifurcation analysis and has been used to recover lineages during early development in mouse embryos from gene expression profiles at multiple time-point measurements.
One adaptation of this technique, Div-Seq, bypasses the need for tissue dissociation by directly sequencing isolated nuclei. As enzymatic dissociation is known to disrupt RNA composition and compromise integrity, studying cells from complex tissues e. Initial approaches for trajectory inference were based on linear paths; however, recent work has integrated the concept of branching 93 , which may be crucial for understanding dynamic cell systems.
Lander and colleagues 94 have recently proposed a more flexible probabilistic framework and utilized this approach to reconstruct known and unknown cell fate maps during the reprogramming of fibroblasts to induced pluripotent stem cells. We expect that additional biological insights gleaned from cell lineage determination or from experiments involving the perturbation of regulators at branching points will be valuable for enhancing our understanding of complex cellular systems.
Even though the primary focus of this article is RNA-seq-based methods, we also note that cellular hierarchy can also be reconstructed from proteomic 95 , 96 or epigenomic measures One can imagine numerous exciting medical applications that can utilize this technology.
Tumor heterogeneity is a common phenomenon that can occur both within and between tumors, and we expect that scRNA-seq can be applied to illuminate unknown tumor features that cannot be discerned from conventional bulk transcriptomic studies.
For example, this technique could be used to assess transcriptional heterogeneity during the development of drug tolerance in cancer cells 98 and to analyze the expression profiles of specific pathways Fig. In this way, scRNA-seq may help generate models of cancer evolution. Additionally, this technique could also be applied to reconstruct clonal and phylogenetic relationships between cells by modeling transcriptional kinetics We further anticipate that RNA can be assessed as a part of routine clinical evaluation, and parallel measurements of both genomic and transcriptomic information in the same cell could elucidate the phenotypic consequences of DNA and RNA variants.
Lineage tracing is a long-standing fundamental question in biology aimed at understanding how a single-celled embryo gives rise to various cells types that are organized into complex tissue and organs Fig. As a proof-of-concept, researchers at Caltech have recently developed a method using the sequential readout of mRNA levels in a single cell to reconstruct lineage phylogeny over many generations Another interesting potential application of scRNA-seq includes identifying genes involved in stem cell regulatory networks.
We are just now starting to understand how stem cells are triggered to become functional cells, which is information that is essential for understanding the basic biological processes underlying human health and diseases.
As sequencing costs decrease, it will be possible to routinely analyze more than a million cells within the next 5 years The Human Cell Atlas , which aims to map 35 trillion cells from the human body, has already started a few pilot studies. The initial plan is to sequence all RNA transcripts in 30 million to million cells and then use gene expression profiles to classify and identify new cell types.
It is anticipated, for example, that scRNA-seq of highly diverse immune system cells will deepen our understanding of their inherent heterogeneity, particularly regarding lymphocyte behavior.
A study from the Broad Institute has further highlighted the utility of scRNA-seq by uncovering a subset of 18 seemingly identical immune cells that show stark differences in gene expression patterns from cell to cell Several emerging scRNA-seq studies have focused on deepening our understanding of cells in the brain , It is likely that the information gleaned from these analyses can be utilized to identify novel pathways involved in neuro-related diseases, providing new therapeutic targets for biomarker discovery.
We envision that future applications of scRNA-seq in biology and biomedical research will also provide novel insights into physiological structure—function relationships in various tissue and organs. Ultimately, with improvements in the availability of standardized bioinformatics pipelines, this work will reveal novel insights into biological systems and create new opportunities for therapeutic development.
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