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What are the different, high-level programs along which a eukaryotic animal cell can follow?

What are the different, high-level programs along which a eukaryotic animal cell can follow?


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What are the different, high-level, disjunct (mutually exclusive at one particular point in time) programs or pathways along which a eukaryotic animal cell can follow? Examples of programs would include growth, cell division, senescence and quiescence. Are there programs that differ between cell types?

Any I'm missing? If so, references much appreciated.


To see the width of your question, have a look at what the Gene Ontology considers a cellular process:

http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0009987#term=children

I don't think you can agree on what's high-level, so it's better to see them all, I think. Also, for completeness, there is a list with cell types which is admirably maintained:

http://en.wikipedia.org/wiki/List_of_distinct_cell_types_in_the_adult_human_body


I'm going to answer my own question with suggestions collected from the comments.

A multipotent stem cell:

  • Growth
    • Growth and clonal division
    • Growth, division and differentiation
  • Division and no growth

A differentiated cell:

  • Senescence (irreversible)
  • Programmed cell death
    • Apoptosis.
    • Autophagic cell death.
    • Necrotic cell death.
  • Quiescence (reversible)
  • Growth ==> Immortality (cancer cells)
    • Growth and division
    • Growth and no division (endocycles)1
  • Division and no growth

1: Norman Zielke, Kerry J. Kim, Vuong Tran, Shusaku T. Shibutani, Maria-Jose Bravo, Sabarish Nagarajan, Monique van Straaten, Brigitte Woods, George von Dassow, Carmen Rottig, Christian F. Lehner, Savraj Grewal, Robert J. Duronio, and Bruce A. Edgar: Control of Drosophila endocycles by E2F and CRL4Cdt2


7.3: Mitotic Phase - Mitosis and Cytokinesis

  • Contributed by Suzanne Wakim & Mandeep Grewal
  • Professors (Cell Molecular Biology & Plant Science) at Butte College

Can you guess what this colorful image represents? It shows a eukaryotic cell during the process of cell division. In particular, the image shows the nucleus of the cell dividing. In eukaryotic cells, the nucleus divides before the cell itself splits in two and before the nucleus divides, the cell&rsquos DNA is replicated, or copied. There must be two copies of the DNA so that each daughter cell will have a complete copy of the genetic material from the parent cell. How is the replicated DNA sorted and separated so that each daughter cell gets a complete set of genetic material? To answer that question, you first need to know more about DNA and the forms it takes.

Figure (PageIndex<1>): Dividing cell stained with fluorescent dyes. You can see chromosomes in blue and spindles in green.


From nutrient supply to growth rate

The multivariate analysis examines the response of yeast cells to different nutrition conditions and over differing growth rates. Cells were cultured in media limiting for either glucose, ammonium, phosphate, or sulfate while the growth rates were set at doubling times of either 3.5, 7 or 10 hours. This allowed the effects of nutrition to be disentangled from secondary effects associated with altered growth rates (Figure 1a). Effects that were only associated with growth rate were identified as variation that was common to the different growth rate conditions across all limiting nutrients (red in Figure 1a). Effects that were only associated with different nutrient conditions were identified as variation that was specific to a nutrition treatment averaged across different growth rates (green in Figure 1a). Finally, nutrition-specific growth-rate effects were identified as growth-rate effects that were found in specific nutrient conditions (blue in Figure 1a).

Analytical approaches. (a) Multivariate analysis of growth rate and nutrition conditions. Comparing cellular responses to varying growth rates and nutrition conditions allows the dissection of growth-rate effects (red), nutrition effects (green) and nutrition-specific growth effects (blue). (b) Systems-biology analysis of cellular responses. Assaying cell responses at the transcript, protein, and metabolite levels allows the analysis of transcriptional (red), protein expression (green), and metabolic (blue) responses. Comparing the transcription and protein-expression responses allows the inference of post-transcriptional responses (orange). Comparing the protein expression and metabolic responses allows the inference of enzyme-metabolite correlations (purple).

The integrative systems biology analysis involved examining the cellular responses at the transcriptomic, proteomic and metabolomic levels (Figure 1b). The transcriptomic responses were assayed using microarrays, the proteomic responses were assayed using isotope tags for multiplexed relative and absolute quantification (iTRAQ) and the metabolomic responses were assayed using gas chromatography coupled to time-of-flight mass spectrometry (GC/TOF-MS). Comparing responses at the transcriptomic and proteomic levels allows the inference of post-transcriptional regulatory effects (orange in Figure 1b). For instance, post-transcriptional regulation can be inferred for a gene if the protein-level response to a treatment differs markedly from the transcriptional response for instance, a marked protein response in the absence of a transcriptional response. Finally, comparing the responses of specific metabolites to the responses of the proteins involved in their metabolism allows correlations between metabolites and cognate enzymes to be explored (magenta in Figure 1b).

In an earlier study Oliver's group identified a response to altered growth rates that was common across nutritional conditions [7]. The current study [6] examines the nutrition-specific effects, and the nutrient and growth-rate-dependent effects. The analysis of nutrient-specific effects revealed that the cells have distinct responses to limitations of each nutrient, of which the response to carbon (glucose) limitation is by far the most dramatic. At the transcriptional level, around 1,200 genes were up- or downregulated under limiting carbon compared with around 100 to 200 for the other three nutrients. In addition, the Gene Ontology (GO) term annotations of transcripts and proteins responding to carbon limitation are largely distinct from those responding to limitation of the other nutrients. The analysis of growth-rate-dependent effects in each nutrition condition revealed a more robust response, with both a greater number of genes involved (around 1,400 to 3,300 across all nutritional conditions) and a greater range of responses at the transcriptional and protein levels. In this case, the GO annotations of the responding transcripts and proteins were similar across all four nutrition conditions and prominent functions included ribosome- and translation-related functions. Again, only a handful of genes were found to be outliers in terms of proteome/transcriptome comparisons.

The integration of transcriptomic, proteomic and metabolomic data provides a more systems-wide view of the cell state than one type of data can. Although all the assays aimed at being as comprehensive as possible, only the transcriptomic data approach the system-wide level. The micoarrays detected transcripts from 6,084 protein-coding genes, whereas the iTRAQ proteomic data detected peptides corresponding to 1,870 open reading frames (ORFs), and the metabolomic data are restricted to a few hundred metabolites (around 400 metabolites were detected and around 100 unambiguously identified and quantified). Nevertheless, these studies provide insights otherwise not possible when one is limed to one slice of the cell's 'omes'.

By comparing the transcriptional responses to the changes in proteins, Gutteridge et al. [6] were able to infer post-transcriptional effects. They found that the overall correlation between transcriptional and protein expression responses was low, and suggest that this reflects pervasive post-transcriptional regulation. Nevertheless, they identified relatively few genes that met their criteria of notable outliers in the proteome/transcriptome comparisons. For instance, across the nutrition conditions only 11 genes were notable outliers. These included cases of positive- and negative-post-transcriptional control, although the mechanism(s) are as yet unknown. Similarly, correlating changes in metabolites with the enzymes that catalyze their production or consumption allowed inferences regarding metabolic responses. Here the data fall short of the hope for a systems-level picture of the cell's behavior. In most cases there was little correlation between the levels of enzymes and the corresponding metabolites. The authors suggest that this reflects the fact that metabolite levels are controlled by systems-level properties of metabolic pathways, which is reasonable given that it has long been known that metabolite levels are well buffered against changes in enzyme concentrations [9]. Given the sparseness of the metabolomic data, and to a lesser extent the proteomic data, a fuller picture must probably await further technological advances.

This is a rich dataset. The analyses to date have largely focused on a high-level analysis of groups of genes with common GO annotations. This revealed that limiting each of the four nutrients tended to induce responses that were moderate in range, but distinct across the nutritional conditions, with carbon limitation producing a unique and dramatic response. On the other hand, the nutrient- and growth-rate-dependent analysis revealed a wider range of transcriptomic and proteomic effects, but which were qualitatively similar across the nutrient conditions. While this analysis naturally focused on genes of known function as a means to biological interpretation, further mining of the data is likely to be fruitful. For instance, Oliver and colleagues noted in their earlier paper [7] that a significant number of genes that were downregulated at increased growth rate are of unknown function. Can these and related data be used to infer the possible functions of these genes?


Animal Cells

Animal cells are specialized. They have different shapes depending on what job they do within an animal’s body. A nerve cell, for example, looks very different to a fat cell, and both look different to a muscle cell.

The basic parts of the cell, however, remain the same whatever the cell’s function.


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Organelles and Components of Animal Cells

Mediran / Wikimedia Commons / CC-BY-SA-3.0

The following are examples of structures and organelles that can be found in typical animal cells:

    - thin, semi-permeable membrane that surrounds the cytoplasm of a cell, enclosing its contents. - cylindrical structures that organize the assembly of microtubules during cell division. - specialized groupings of microtubules that protrude from some cells and aid in cellular locomotion. - gel-like substance within the cell. - a network of fibers throughout the cell's cytoplasm that gives the cell support and helps to maintain its shape. - an extensive network of membranes composed of both regions with ribosomes (rough ER) and regions without ribosomes (smooth ER). - also called the Golgi apparatus, this structure is responsible for manufacturing, storing and shipping certain cellular products. - sacs of enzymes that digest cellular macromolecules such as nucleic acids. - hollow rods that function primarily to help support and shape the cell. - cell components that generate energy for the cell and are the sites of cellular respiration. - membrane-bound structure that contains the cell's hereditary information.
    • Nucleolus - structure within the nucleus that helps in the synthesis of ribosomes.
    • Nucleopore - a tiny hole in the nuclear membrane that allows nucleic acids and proteins to move into and out of the nucleus.

    Background

    There have been many cell death modes described in the biomedical literature [1,2,3], far more than enough to confuse probably all the experts who dedicate their careers to the research of cell death mechanisms [4]. Those who are not fully dedicating themselves to cell death research must be even more befuddled. Readers of this essay are encouraged to test themselves and ask around whether they or any of their acquaintances are familiar with all of the 34 cell death modes listed below that are collected by us from the literature: accidental cell death [2], regulated cell death [2], senescence, necrosis, regulated necrosis [5, 6], type I cell death [2, 7, 8], type II cell death [2, 7, 8], type III cell death [2, 7, 8], cannibalistic cell death [9], programmed necrosis [10], aponecrosis [11], netosis [12], necroptosis [12, 13], apoptosis, mitochondrial apoptosis [14], intrinsic apoptosis [15], extrinsic apoptosis [15], non-apoptotic cell death [6], non-apoptotic regulated cell death [16], mitotic catastrophe [17, 18], degeneration [19, 20], parthanatos [21], entosis [9, 22], cornification [23], methuosis [24], oncosis [25], paraptosis [26], anoikis [27], pyroptosis [28], ferroptosis [29], phagoptosis [30], caspase-independent apoptosis [31, 32], cell death independent of caspases [33], and excitotoxicity [34, 35]. Besides these 34 demise modes, there must be many other less frequently used terms not listed, of which we are unaware. There are also many other types of cell death that do not belong to any of the abovementioned modes and have not been extensively studied. For instance, in a heartbeat cells can be burnt to death or killed by strong acids or bases, and chewing a grape also kills the grape’s cells instantly in the mouth. Moreover, some cellular activities, including micropinocytosis, macropinocytosis [36], phagocytosis, autophagy, etc., are often considered as cell death mechanisms, although they per se are not cell death but can lead to death of the cells if the activities are severe enough and persistent. As a good example, autophagy is developed to recycle (and thus save) resources via a cellular cannibalism, i.e. consumption of a cell’s own components, for the cell to survive such a situation wherein nutrients are scarce, and, when the cell is cancerous and fast-growing, to build new cells more economically. However, overconsumption of cellular components will lead to cell death.

    Although there seem to be many different ways for cells to die, if we step back and look at cell death more distantly, from the viewpoints of the host tissue or organ or the host animal, we may not be so baffled. Even just looking at the cell per se will be less perplexing than a close-up look at the molecular details. After a long meditation on the relationship between the cell that is about to die and its host tissue/organ or its host animal, which most studies do not emphasize, we extrapolate that there are only four basic cell death modes, including two physiological ones, i.e. senescent death (SD) that is death from cellular aging, and apoptosis, as well as two pathological ones, i.e. necrosis and stress-induced cell death (SICD) [37]. Of course, this classification has culled away those caused by extreme physical or chemical factors, such as the aforementioned “burnt-to-death” one, on which studies may not have much clinical value (although studies of damage by milder physical and chemical factors do have value). Other than these four, the remaining demise modes listed above do exist, but they are ad-hoc variants or amalgams of some of these four basic ones in different situations. The appearance of so many ad-hoc death mechanisms is largely because cells in a creature of evolutionarily high level on one hand have allegiance to the host tissue, or the creature that wants these cells to die for its ultimate best interest, but on the other hand the cells are smart and selfish and try their best to survive all different stressed situations. Restated, the interaction between these two conflicting or paradoxical facets of animal cells leads to the large variety of ad-hoc survival mechanisms and death mechanisms of cells. In this essay we expound our musings on these aspects to challenge several basic notions that have been ingrained in, and have formed the mainstay of, cell death research. Modes of cell replication that are so often associated with cell death are briefly introduced as well.

    Modes of cell proliferation in physiological situations

    In a creature high on the evolutionary “tree of life”, one important feature is that each cell type has a physiological total number. Another trait is that in most organs and tissues, cells come and go by replication and death whereas, in some other cell types such as neurons and cardiac myocytes, cells are no longer capable of replication after the animal reaches a certain age. There are two types of cell replication, i.e. direct proliferation and compensatory proliferation [38,39,40,41]. In humans, direct proliferation occurs during body growth before and during puberty or occurs in some special situations, such as in obesity that requires more adipose cells to store extra fat, or in pregnancy during which cell proliferation occurs in the uterine and mammary tissues. Compensatory proliferation, commonly referred to as “regeneration”, occurs when some cells have reached the end of their lifespans, i.e. when cells die from aging, which is defined herein as SD, and thus the host tissue or organ needs new cells to make up the physiological number of cells. Some people estimate that in a human body 60 billion cells die every day [42], although some others estimate that one million cells die every second [43,44,45,46], which is 86.4 billion cells per day. Of course, some of these many deaths may be due to a pathological reason such as SICD that will be described later. Therefore, the human body needs to yield 60–86.4 billion new cells per day to compensate for the cell loss.

    Modes of cell death in physiological situations

    In an animal of evolutionarily high level, physiologically there are only two major modes of cell death, i.e. apoptosis and SD. The term “apoptosis” was given by Kerr et al. in 1972 [47], but this type of cell death was described over one and half centuries ago [8, 48], although the descriptions by different research-ancestors were not quite the same. In evolutionarily high animals, many cells are no longer needed during or after certain developmental or physiological states, such as during digit individualization in the human embryo, post-pubertal involution of the thymus, postpartum involution of the uterus, post-lactating (post-weaning) involution of mammary glands, etc., as some of us have reviewed before [37, 49]. Apoptosis is the mechanism used by the animal to get rid of these cells that are no-longer useful to it and thus are redundant. The animal requests these obsolete cells to die via a pre-determined procedure, or a “program”, thus making this death mode regarded as a “programmed cell death”.

    One hallmark of apoptosis is that the cell death is physiological and should not cause any harm to the host tissue and certainly not to the entire organism. In animals, this is achieved by mobilizing macrophages or other cells that have phagocytic ability, collectively coined as “scavenger cells” [49, 50], to engulf the dying or dead cell before its decomposition to dregs that contaminate the host tissue environment and release immunogenic materials to incite inflammation. This phagocytosis occurs actively and requires communication between scavengers and the cell which is to die, dubbed as “apoptoting cell” by some of us [49], via such as “find-me” and “eat-me” signals [50] and via other signals from the apoptoting cell to promote the scavengers’ survival [51] and migration [52]. This phagocytosis of apoptoting cells as an iconic feature of apoptosis was first described by Kerr et al. [47] as well as by Schweichel and Merker [7], but recently it seems to have been studied again in more detail under the umbrella of “entosis” [9]. Sending out “find-me” and ‘eat-me” signals from apoptoting cells to scavengers indicates that apoptosis is a suicidal event. Moreover, these traits also mean that apoptosis has fully evolved only in those animals equipped not only with macrophages that have a huge capacity for phagocytosis but also with blood and lymphatic circulation systems that allow macrophages to migrate from distant sites to the suicidal cells. However, considering apoptosis “evolutionarily developed” also acknowledges that simpler apoptosis mechanisms should already have existed in those animals lower on the life tree. Indeed, caenorhabditis elegans has no blood nor lymphatic circulation system but already has an apoptosis mechanism, since the dying or already-dead cells can be engulfed by their neighboring cells [53]. Because carcinogenesis can be regarded as an atavistic process, a tumor can be regarded as an evolutionarily-lower organism that parasitizes the host patient [37, 54, 55]. Therefore cancer cells in a tumor lump live “physiologically” in the host body and may have an apoptosis mechanism simpler than that in the patient’ cells. Nevertheless, complex communication and coordination between a predator and its prey implies that a fully developed apoptosis is a highly programmed event, which is initiated by a motivation of the animal’s body to eliminate outmoded cells and is terminated at the complete clearance of the cell corpse inside the scavenger, with preservation of the host tissue environment as the basic pre-condition [37, 49, 50, 55]. For example, after pups wean, lactating mammary epithelial cells no longer have value to the dam and thus need to be purged from the breast, but this massive cell death should not be detrimental to the dam, i.e. should not cause inflammation and scar formation in the breast. Any mode of cell demise sans this motivation and this corpse clearance but with inimicality to the host tissue is not an authentic and fully-developed apoptosis, which, unfortunately, is rarely emphasized as one of the icons of apoptosis in relevant publications. Actually, as has been repeatedly wrangled before by some of us [37, 49, 50, 55], pure apoptosis occurring in such as aforementioned in vivo models has received little attention because most studies avowed to be on apoptosis are virtually on SICD [37] that will be described later.

    In an animal such as in the human, all normal cells, without exception, undergo a three-phased aging procedure, i.e. (1) proliferation for a certain number of cycles, (2) loss of the replication ability and then quiescence for a certain period of time, (3) and then dying and death. This means that all normal animal cells have lifespans, although the lifespans of different cell types are different. For instance, the lifespans for presumptive naive T cells (phenotype CD45RA+) and memory T cells (CD45RO+) in the human are calculated to be 3.5 years and 22 weeks, respectively [56]. Some cell types in the human, such as neurons and cardiac myocytes, lose their proliferation ability during childhood but then have the longest lifespans, basically living until the person dies. This usually means that these cells have a strong ability to resist various stress insults during the decades of the person’s life. Partly due to this advantage, i.e. this resistance, those cells that have lost replication ability do not develop tumors (tumors originated from heart muscles and neurons were initiated during the embryonic stages and are manifested as childhood diseases) [40, 41, 54, 55, 57]. On the other hand, some other cell types such as keratinocytes in the skin and mucosal cells in the gastro-intestinal tract have relatively short lifespans, i.e. die quickly, but meanwhile they also have a strong ability for regeneration to make up for the quick cell loss, collectively manifested as a high rate of cell turnover [54, 58, 59]. Actually, in many organisms including bacteria, slowly-proliferating cells survive better than their fast-proliferating counterparts [54, 60]. This hypothetical reciprocal relationship between the lifespan, on the one hand, and the ability to regenerate and to resist stress on the other hand, as summarized in Fig. 1, deserves more thorough research.

    Hypothetical reciprocal relationship between the lifespan on one hand and the abilities to regenerate and to resist stress on the other hand. The abilities of immortalized cells (such as cancer cells or cell lines) to regenerate or resist vary greatly, depending on the cell types, but they should not undergo SD

    Cellular aging is often referred to as senescence, the meaning of which, however, is often ambiguous in the literature, as many peers define it as “irreversible growth arrest” [61], which does not necessarily mean that the cell will die. To avoid equivocality, we refer to cell death from aging as SD. Since in apoptosis it is those no-longer useful cells that die, those cell types that have lost regeneration ability but have long lifespans may not die from apoptosis because they are, in fact, useful, or, more correctly, indispensable. Instead, since the host creature wants these very useful cells to live and function as long as possible, they can only die from SD in a physiological situation, besides the pathological death that will be narrated later. Cells that die of SD will also be gulped down by scavenger cells, just like apoptotic cells, and thus should not be inimical to the host tissue. Of course, those apoptotic or senescent cells that reside on a body surface (such as in the skin) or near a cavity (such as in the intestinal tract) will directly fall out and thus will not be scavenged. These cells will not be discussed herein, as a caveat already has been given before [50].

    Absence of apoptosis in cell culture

    As some of us have repeatedly addressed before [37, 49, 50, 55], for several reasons an authentic apoptosis as above defined never occurs in cell lines cultured in Petri dishes. First, cell lines are all immortalized, established by reprogramming the death program of the parental cells [57], whereas study of apoptosis is for the purpose of determining the original, unchanged death program. Actually, in our opinion, all immortal cells, including all tumor cells, do not have a death program because they do not have a lifespan, according to the definition of “immortality”, and thus cannot die from a programmed procedure with suicide as its essence. Even if, as described in so many publications, immortal cells still have a death program established by reprogramming the normal cells’ death program, studies using these cells with an already-changed death program can only provide us with already-altered mechanisms. More complicatedly, different cell lines, no matter whether they are derived from spontaneous tumors or are manmade in the lab using such as viruses, are immortalized via different mechanisms, as summarized before by one of us [57]. Therefore, different cell lines will have differently-reprogrammed death programs and will likely provide us with different mechanisms or pathways of cell death. This is one of the reasons why so many demise mechanisms have been identified, and likely many more are waiting for us to identify them, although in our opinion most of these mechanisms are actually ad hoc variants of SICD that will be described later. Second, a genuine apoptosis is initiated for a twofold purpose, i.e. clearance of useless and thus redundant cells under a condition of preserving the host tissue in an intact status. However, cell lines are autonomous and thus no longer allegiant to the host tissue and animal and, in a culture dish, have no reason to care about whether their environment is polluted or not by their cellular shreds. In short, cell lines in Petri dishes have no motivation to keep their environment undisturbed. Third, most cell culture systems used for apoptosis studies involve only one single cell line in the Petri dish, thus lacking scavenger cells and in turn lacking complex communications among different cell types. These missing communications include those between apoptoting cells and scavengers via such as “find-me” and “eat-me” signals, between apoptoting cells and their healthy sibling cells and even cells in distant organs to “discuss” which and how many cells are really redundant and need to be eliminated, and between the non-apoptoting cells and scavengers via such as “don’t eat me” signals to protect useful siblings from being mistakenly predated by scavengers [50]. Fourth, apoptosis consists of two parallel procedures, one occurring in the suicidal cell and the other in the scavenger [50]. The mid and later parts of apoptosis occur inside the scavenger and involve its enzymes to dispose of the prey. These two procedures, each in a different cell but in parallel with the other, are highly coordinated via the aforementioned cell–cell communications even before the suicidal cell is wolfed down by the scavenger. In those studies with only one single cell line as the only player in the culture dish, one procedure is lacking, making impossible the coordination between the two. Because of these reasons and some others that have been mentioned before [50], even if a programmed cell death occurs in vitro as described in so many publications, it occurs in an unusual situation, study of which can only provide us with unusual mechanisms and pathways that do not actually occur in an animal’s body [50]. At least, in our body there normally is no any single immortal and autonomous cell, and thus the mechanisms identified in cell lines have no relevance to normal persons, while we should keep it in mind that apoptosis is evolutionarily developed, and thus is a mechanism for the normal.

    Modes of cell proliferation in pathological situations

    In pathological situations, animal cells may proliferate without a need for compensation for cell loss, resulting in hyperplasia, which is a pathological phraseology for the existence of extra (redundant) cells, usually with enlargement of the affected organ as a sequel. For example, some chemicals such as phenobarbital [62, 63] or lead nitrate [64] can induce proliferation of hepatocytes, resulting in liver enlargement [41]. Aberrant expression or mutation of some genes, usually oncogenes, may also coerce the affected cells to replicate directly [55]. Direct proliferation occurring in these situations is a pathological event and, as it results in an excess of cells, apoptosis ensues as a recovery procedure to remove the redundant cells [40, 41]. For this reason, many transgenic mice expressing a proliferation-driving oncogene show high proliferation rates but low carcinogenic efficiencies, because many mutation-bearing cells have been swept out via apoptosis soon after they were produced [38, 40, 41, 65]. It goes without saying that benign or malignant tumor cells can also proliferate continuously, as tumor in pathology textbooks is defined as “uncontrolled cell growth”, or “autonomy in replication”.

    Modes of cell death in pathological situations

    Severe stress can kill cells instantly, and it usually is an exogenous stress, such as a bacterial infection or an infarction in which blood supply to part of an organ is blocked. Cell death resulting from a harsh stress usually abounds, occurs within a short spell, and does not require participation of scavenger cells, unlike apoptosis and SD. However, when cell corpses have decayed to smithereens and then release immunogenic components, scavenger cells will be mobilized to engulf the cellular dregs as part of the inflammation. This type of cell death is called necrosis, which has been well delineated in pathology textbooks for centuries. Necrosis as a pathological event commences with many irreversible changes in the nucleus, mitochondria and other organelles of the affected cells. After these cellular changes, the necrotic cells may merge, making the outlines of individual cells indistinct and together often forming a focus of coarsely granular, amorphous, or hyaline material. Common types of necrotic lesions that need to be taught to every medical student worldwide are shown in Fig. 2.

    Several common necrosis types in human tissues. a An area of liquefactive or lytic necrosis from a lung abscess, which is fraught with inflammatory cells. b An area of coagulative necrosis from a kidney infarction showing that all necrotic cells have lost their outlines and cellular morphology but the renal histology still remains intact. Note that there are few inflammatory cells infiltrating into this large necrotic area. c An area of caseation necrosis from a tuberculous lymph node showing the lack of massive infiltration of inflammatory cells. d An area of fibrinoid necrosis from a heart with rheumatic disease showing the lack of extensive infiltration of inflammatory cells

    Sometimes, a stress, especially when derived from the cell per se, may not be taxing enough to cause immediate cell death but may be capable of turning on some intrinsic suicidal mechanism of the cell. This mode of cell demise is referred to as SICD [37]. For example, during physiological cell turnover, i.e. when cells are regenerating to compensate for those that have died of aging, i.e. SD, DNA mutation may occur as a contingency in some proliferating cells. The cell will first arrest its proliferation, usually at the G1 or S phase of the cell cycle, to repair the DNA. However, sometimes the mutation is irreparable in this case, the cell usually turns on a demise program to commit suicide, so that the mutation will not be passed to progeny cells to be hereditary. It goes without saying that chromosomal fragmentation [66,67,68] or other forms of mitotic catastrophe [17, 18], with much greater genomic damage than single mutations, are extreme examples of this type of SICD that are usually discerned in cancer cells. Sometimes blood cells as frontier fighters against micropathogens like bacteria and viruses are infected by bacteria or viruses but cannot eliminate them. In this case the cells will turn on a death program to commit suicide, so that they will not carry and thus spread the pathogens to other body sites [54]. This “kill your foe or kill yourself” phenomenon, which is often seen in movies, occurs daily in our body. Similar to such micropathogen infections, there are many other types of exogenous stress that are severe but still insufficient to kill cells instantly and thus trigger an endogenous stress to initiate SICD. This is typically discerned in patients receiving radiation or some chemotherapeutic agents that cause substantial DNA damage not only in cancer cells but also in some normal cells the damaged DNA in turn serves as an endogenous stress to precipitate SICD. In a nutshell, many cells in those animals higher on the life tree have an allegiance to the animal’s body and will die via SICD, if such sacrifice is needed to maintain the life of the animal in a stressed situation, which is a common trait, acquired evolutionarily, of many organisms, especially in the animal kingdom [37, 54, 55].

    When stress induces death of only a small number of cells, scavenger cells are able to purge them all from the tissue or organ. This situation resembles apoptosis and thus is dubbed as “stress-induced apoptosis-like cell death (SIaLCD)” [37]. Actually, it may be possible that the number of necrotic cells is small as well, since sometimes harsh stress may affect only a few cells and not necessarily kill many. Moreover, the necrotic cells may be scavenged before they decompose to cellular dregs, making necrosis indistinguishable from SIaLCD. However, necrosis is still a homicide, since the cells are killed, but do not die from an intrinsic suicidal program. In addition, this engulfment may be an action of macrophages alone and may not involve signals such as “find-me” and “eat-me” from the dying cells, thus differing from that in apoptosis. The fact that all multicellular animals have an intention to minimize the deleterious effect of dead cells on their bodies makes macrophages dual-functional in inflammation: on one hand they are one of the important inflammatory components. On the other hand they function to prevent inflammation from occurring by swiftly gobbling up dying or dead cells to prevent putrefaction of cell corpses to cellular shards. When cells that die of SICD are superabundant and inundate scavenger cells, many cell corpses will decompose and release various immunogenic cellular materials to agitate inflammation, first locally and then systemically. This subtype of SICD is coined as “stress induced necrosis-like cell death (SInLCD)” [37].

    Because in necrosis and SICD it is those useful cells that die, the unaffected normal cells will regenerate to compensate for the cell loss and to heal the wound. In both necrosis and SInLCD, sometimes the cell death is massive and persistent and goes beyond the regeneration capacity, in such as chronic hepatitis B virus infection wherein the viruses not only constantly kill hepatocytes but also impede the regeneration of the still-alive hepatocytes. In this situation, cells of connective tissue, mainly fibroblasts, will step into help the wound-healing by forming a scar, which in the liver infected by the hepatitis B virus manifests as cirrhosis. Generally speaking, regeneration and wound healing follow SCIaLCD, SCInLCD and necrosis but scar formation may only follow SInLCD and necrosis, due to an immense loss of useful cells [37].

    The actual meaning of the well-characterized caspase-cytochrome c pathway

    The above-described SICD has been well-characterized but, haplessly, it is misconstrued as apoptosis in most relevant studies. Indeed, the caspase-cytochrome c pathway of cell death has been widely accepted as a typical apoptosis pathway. However, several issues of this pathway have been neglected: at its physiological location (the inner membrane of the mitochondrion), cytochrome c (Cyt-c) participates in ATP production to power the cell, thus sustaining the cell’s life and making it actually an oncoprotein. Only when mitochondrial permeability is changed, causing leakage of Cyt-c from the inner membrane to the cytoplasm, which is a purely pathological (stressed) event and is likely induced by a form of stress (such as a chemo drug), does it cause cell death and only then does it function as a tumor suppressive protein [69]. In other word, the caspase-Cyt-c pathway not only is caused by a stress but also requires relocation of Cyt-c from its normal cellular location to an abnormal one wherein, and only wherein, it can bind to other death-driving proteins to cause cell death [69]. Thus, it occurs only in a pathological situation. Little, if any, evidence has been shown that (1) Cyt-c can cause death without a form of stress involved, such as a culture condition wherein usually only 10% serum is available, (2) Cyt-c leaking-out from the mitochondrial inner membrane can also be a physiological event, and (3) at its physiological location (within the inner membrane of mitochondrion) Cyt-c can cause cell death as well. Actually, other than Cyt-c, there are many proteins that are compartmentalized in a sort of organelle of the cell because they function differently in physiological and pathological situations lysosomal enzymes are another example, as the enzymes will digest out the cell and kill it once they have leaked out from the lysosome to the cytoplasm. Therefore, the well-characterized caspase-Cyt-c pathway of cell death is actually a mechanism of SICD, but not of apoptosis, in our opinion [69]. However, much of the literature is correct about that it is indeed a “mechanism of cancer remedies” that, in our opinion, is SICD and not apoptosis, either. Of course, it remains possible that apoptosis lends its mechanism to SICD to deal with various pathological situations, and we just don’t know it, since studies on true apoptosis are very insufficient with such aforementioned in vivo models as post-weaning involution of mammary glands and postpartum involution of the uterus [50]. In other words, it is currently unclear whether SICD borrows the death program from apoptosis or uses one different from that of apoptosis.

    We are all familiar with a phenomenon that a stressful life ages people more quickly. Therefore, stress, even when it is too mild to directly kill cells via necrosis or SICD, may be an impetus for cellular aging leading to SD, probably in part by affecting telomere length [70]. We opine, with trepidation, that with the extent of stress increasing, the same form of stress to the same type of cell will first prod SD, and then SIaLCD, followed by SInLCD and necrosis, as depicted in Fig. 3.

    Relationships between different extents of stress and different cell death modes. Very mild stress may impel cellular aging, leading to an earlier SD of the affected cells. Stress may also hasten apoptosis, although this conjecture still lacks concrete supporting evidence since few in vivo studies focus on unadulterated apoptosis. A stronger stress may cause SIaLCD and an even stronger stress may cause SInLCD with more dead cells exceeding the clearance capacity of scavenger cells and decaying to cellular shards to agitate inflammation. A severe stress will directly kill cells via necrosis

    Similarities and disparities among apoptosis, necrosis, SICD and SD

    Apoptosis as a suicide, and necrosis as a homicide, are irreconcilable to each other. SICD as another death mode resides between apoptosis and necrosis with many similarities and disparities to the two, as summarized in Fig. 4 and Table 1, often causing confusion or being mistaken as apoptosis or necrosis. First, SICD occurs to the useful cells and is a pathological event, which resembles necrosis but starkly contrasts with apoptosis. Second, because in SICD it is the useful cells that die, cell regeneration, wound healing and probably also scar formation ensue, which again resembles necrosis but contrasts with apoptosis that eliminates archaic cells and therefore does not trigger regeneration. Because of the need for regeneration and wound healing, SICD involves complex communications between the dooming cells and the surrounding healthy cells on such important issues as how many cells need to be regenerated, when and where the minted cells should emerge, as well as whether fibroblasts need to step into help heal the wound. Although necrosis is also followed by regeneration, its homicidal nature and the resulting swiftness of cell death may not allow for such complicated cell–cell communication. Since SICD is a programmed suicidal procedure, it resembles apoptosis by enticing scavenger cells to dispose of the cell corpse via complicated communications between the predator and the prey to coordinate the time and the location of the predation. Both apoptosis and SICD may involve communications between the dying cells and their healthy siblings, but this aspect has gained little attention and few explorations. Third, if in SICD the death tally is exceedingly high and goes beyond the clearance capacity of scavengers, i.e. in a situation of SInLCD, inflammation succeeds as aforementioned, which resembles necrosis but differs from apoptosis. Fourth, apoptosis can only occur in vivo but SICD and necrosis can occur in cell culture as well. Actually, most mechanisms and pathways described in the literature for “apoptosis” have involved stress of every kind, cell lines of every type and cell culture systems of every sort, and therefore are actually for SICD, as aforementioned. Reiterated more clearly, SICD is well studied with much of the mechanism(s) well illustrated from cell lines in culture while unadulterated apoptosis is poorly studied with the mechanism(s) largely unknown.

    Illustration of the relationships among apoptosis, SD, SICD and necrosis. It is the healthy but useless cells that undergo apoptosis, whereas it is the useful but damaged cells that die of SICD (either sIaLCD or SInLCD) or necrosis. Useful cells, either healthy or damaged ones, can age and eventually die of SD, but whether obsolete cells also undergo SD is an intriguing question that remains murky, because these cells may be removed much more efficiently via apoptosis. Apoptotic and SIaLCD cells will be phagocytosed whereas SInLCD and necrotic cells will decompose to cellular dregs that cause inflammation. Moreover, SInLCD resembles necrosis that will cause regeneration and wound healing, probably in association with scar formation, but these activities do not follow SIalCD and apoptosis

    SD is a suicide of useful cells, which resembles SICD but differs from apoptosis. Because of the neat coordination in the living body, the tally of death from SD should not be so high as to glut the scavengers’ capacity. Therefore, usually SD is not associated with inflammation, which resembles apoptosis and SIaLCD but differs from SInLCD and necrosis. For those cell types that retain a regeneration ability, regeneration follows SD as it is the useful cells that die, making SD similar to SICD and necrosis but dissimilar to apoptosis. Since, as aforementioned, apoptosis, as well as regeneration following SD, SICD and necrosis, require different spectra of cell–cell communication and interaction, SD has similarities and differences with apoptosis, SICD and necrosis in this aspect.

    Many cell death modes and survival pathways as ad-hoc variants

    In our opinion, of the many cell death modes described in the literature, some are ad-hoc variants of apoptosis or SD in different physiological situations, while most others are ad-hoc variants of SICD in different pathological situations or in different cell lines because SICD resides between apoptosis and necrosis. For instance, cornification is apoptosis occurring in skin [23], whereas SICD is a better idiom to summarize such death modes as “regulated necrosis”, “necroptosis”, etc., that manifest both necrotic and apoptotic features. Cells often die via SICD, because they always try to utilize all possible means to survive a particular stress although they still die eventually because their death is due to the organism’s iron will to deal with the particular stress or because they cannot defy the stress. Owing to this property of “using all available mechanisms to survive a particular situation”, cells survive initially and then die differently among different particular situations, creating many ad-hoc survival pathways and in the meantime leaving us with many ad-hoc modes of cell death. For example, pyroptosis is SICD of macrophages in which pyrogens can be released to cause hyperthermia [28]. The parlances like “caspase-independent apoptosis” and “cell death independent of caspases” may be superfluous, since we surmise that authentic apoptosis in an animal may indeed not involve caspases originating from the dying cell itself, because macrophages as professional cell disposers have professional enzymes, including caspases, to dispose of their prey [50]. Although few studies have been conducted to explore the mechanisms of authentic apoptosis in vivo, there is some in vivo evidence supporting this conjecture: post-weaning involution of mouse mammary glands does not show aberrant activation of caspases and their downstream effector protein PARP-1 [71], and still occurs normally in caspase-3 knockout mice [72]. Moreover, apoptotic death of mammary tumor cells in c-myc transgenic mice is actually associated with a decreased expression of Cyt-c [73]. However, a caveat needs to be given that these many ad-hoc variants of the four basic cell death modes are still meaningful and worth exploring as they reflect cell death, mainly SICD, at different particular circumstances, understanding of which is an important scientific footing for precision medicine or personalized medicine.

    Stress can directly kill cells (necrosis), can turn on intrinsic death program of cells (SICD), and can goad aging-caused cell death (SD), depending on the extent of stress and the cell type, as different cell types can withstand different extents of stress. For instance, as an adverse event, a given radiotherapy or chemotherapy can directly kill some normal cells (necrosis) but can only cause SICD or spur SD of some other normal cells while having no effect at all on a third set of normal cells, creating heterogeneity of cell death in a given tissue or organ. Actually, heterogeneity of cell death is a common phenomenon when a tissue encounters a strong stressor [74]. It is also possible that a given stress causes death of the same cell via combined mechanisms, including SD, SICD and necrosis. In our cogitation, it is not that necrosis can also be a programmed event but it is because SICD is misconstrued as necrosis. Also, it is not that apoptosis may be immunogenic as well, as alleged in many studies [2], but it is because SICD is misconstrued as apoptosis.

    Remaining conundrums

    All animals, including humans, have been programmed in their nuclear and probably also mitochondrial genomes to die eventually, and all cells in an animal will die along with the animal itself, if not earlier. There hitherto has not been any way to immortalize an animal, and not even an organ, but individual cells can be easily reprogrammed to be immortal, either spontaneously as bespoken by benign or malignant tumor cells appearing in humans, or intentionally as cancer researchers often do in labs. Therefore, the program of cellular SD is not the program of aging of the organ or the animal. A related question that is still under debate is whether prokaryotic and unicellular eukaryotic cells undergo aging, since these unicellular organisms, typically bacteria, maintain their species by constant cell division [58, 75]. Cancer cells are immortal and, even after the patient has died, can survive perpetually as cell lines, in which situation individual cancer cells resemble such unicellular organisms as bacteria that keep dividing to maintain themselves. What still awaits clarification is whether cancer cells and even benign tumor cells also age, and thus also undergo SD, since in so many studies senescence is another nomenclature of cellular aging and since there are plentiful publications describing senescence of cancer cells [76]. Reporting SD of tumor cells, spontaneously or induced by an implementation, seems to oppose their immortal nature and thus seems preposterous, because it says that “immortal ones will still age and die of aging”. Alternatively, one can strictly define “senescence” as “irreversible growth arrest” and disconnect it from cellular aging and cell death. In our logic, stress of any kind, such as an irradiation or a chemotherapy, is unable to induce or accelerate SD of immortal cells, such as cancer cells and various cell lines, either in vivo or in vitro, although it can kill these cells via necrosis or SICD. Restated, a remedy causes only SICD or necrosis, but not SD, of cancer cells that are immortal.

    We are also contemplating over whether apoptosis, SD and SICD are really programmed events as stated in this and almost all other relevant articles. A program is a pre-determined procedure, which in our opinion opposes the fact that most cells in animals are very plastic and can easily adapt to different changes in their microenvironment with a purpose for survival or for a better life, just like those of us who crave for a better life and increased longevity. The fact that there have been so many ad-hoc modes of programmed cell death identified demonstrates the extreme flexibility of demise programs. If a program can be changed easily, i.e. can adapt easily to every slight change in the microenvironment, it is actually not a program that is pre-determined.

    Another question over which we have for long been pondering is whether apoptosis as a pure physiological event developed evolutionarily is encoded by a cellular structure, irreversible change of which is responsible for the irreversibility of the cell death procedure. Or is apoptosis just like aging and type 2 diabetes that, unlike most other biological functions, lack a structural basis as some of us have wrangled before [58]? This is because no such cellular structure has been identified yet that is uniquely responsible for authentic apoptosis.

    What bedevils us the most is such a notion that necrotic cells putrefy to release immunogenic cellular materials to instigate inflammation. Although this is true in lytic necrosis and probably at a late stage of some other types of necrosis, Fig. 2 shows a very striking phenomenon in which there rarely are immune cells in large areas of common necrosis types, even when all necrotic cells have already lost their outlines and have fused together. This trait seems dissonant with the above description that inflammation is one of the consequences and hallmarks of necrosis, but few articles discuss this incongruity.


    You write, “The tension between the individual and the group is the fundamental tension of life.” Unpack that idea for us.

    I’m so happy you asked that! Nature demands variation in physiology and behavior. I argue that behavior is a driving force, because we’ve shown how behavior can influence the ecology of a species and its ability to expand its range in order to survive in different circumstances. Without variation, there is no survival as the environment changes. And this means we need to have a lot of individuals.

    The other thing nature demands is cooperation. We can see that in everything from the basic eukaryotic cell to human society. We have these two dichotomous issues: the demand to be individual, with this bell curve of personality type ranging from aggressive to timid, and the need to cooperate. If somebody is asocial, as we see in some animals or people, that could be good in some situations. But if you’re too asocial, you can’t cooperate and you’ll be doomed. Nature is an optimization process and we should be cognizant, both among humans and other animals, how to best optimize our level of diversity while also allowing cooperation.


    On eukaryotic intelligence: Signaling system's guidance in the evolution of multicellular organization

    Communication with the environment is an essential characteristic of the living cell, even more when considering the origins and evolution of multicellularity. A number of changes and tinkering inventions were necessary in the evolutionary transition between prokaryotic and eukaryotic cells, which finally made possible the appearance of genuine multicellular organisms. In the study of this process, however, the transformations experimented by signaling systems themselves have been rarely object of analysis, obscured by other more conspicuous biological traits: incorporation of mitochondria, segregated nucleus, introns/exons, flagellum, membrane systems, etc. Herein a discussion of the main avenues of change from prokaryotic to eukaryotic signaling systems and a review of the signaling resources and strategies underlying multicellularity will be attempted. In the expansion of prokaryotic signaling systems, four main systemic resources were incorporated: molecular tools for detection of solutes, molecular tools for detection of solvent (Donnan effect), the apparatuses of cell-cycle control, and the combined system endocytosis/cytoskeleton. The multiple kinds of enlarged, mixed pathways that emerged made possible the eukaryotic revolution in morphological and physiological complexity. The massive incorporation of processing resources of electro-molecular nature, derived from the osmotic tools counteracting the Donnan effect, made also possible the organization of a computational tissue with huge information processing capabilities: the nervous system. In the central nervous systems of vertebrates, and particularly in humans, neurons have achieved both the highest level of molecular-signaling complexity and the highest degree of information-processing adaptability. Theoretically, it can be argued that there has been an accelerated pace of evolutionary change in eukaryotic signaling systems, beyond the other general novelties introduced by eukaryotic cells in their handling of DNA processes. Under signaling system's guidance, the whole processes of transcription, alternative splicing, mobile elements, and other elements of domain recombination have become closely intertwined and have propelled the differentiation capabilities of multicellular tissues and morphologies. An amazing variety of signaling and self-construction strategies have emerged out from the basic eukaryotic design of multicellular complexity, in millions and millions of new species evolved. This design can also be seen abstractly as a new kind of quasi-universal problem-solving ‘engine’ implemented at the biomolecular scale—providing the fundamentals of eukaryotic ‘intelligence’. Analyzing in depth the problem-solving intelligence of eukaryotic cells would help to establish an integrative panorama of their information processing organization, and of their capability to handle the morphological and physiological complexity associated. Whether an informational updating of the venerable “cell theory” is feasible or not, becomes, at the time being – right in the middle of the massive data deluge/revolution from omic disciplines – a matter to careful consider.


    Requirements for the Major

    Students must complete a minimum of 31 credits of Biological Science courses as detailed below. Unless specifically stated otherwise, courses may not be used to meet multiple requirements of the major.

    In addition to the standard Biology major, there are two Named Options: Biology with a Named Option in Evolutionary Biology and Biology with a Named Option in Plant Biology. Admissions to the Named Option in Plant Biology is suspended as of Fall 2021.

    Students may complete only one Biology major/named option and must declare the named option they are pursuing.

    Core Requirements

    Mathematics and Statistics

    Chemistry

    Physics

    Introductory Biology

    For AP Biology policy, as it applies to introductory biology in the biology major, see this link.

    Foundation Course (complete one of the following):

    Students may use BIOCORE 381 and BIOCORE 383 toward bothIntroductory Biology andFoundation.

    Course List
    Code Title Credits
    AGRONOMY/​HORT 338 Plant Breeding and Biotechnology3
    BIOCHEM 501 Introduction to Biochemistry3
    BIOCHEM 508 General Biochemistry II3-4
    BIOCORE 381
    & BIOCORE 383
    Evolution, Ecology, and Genetics
    and Cellular Biology
    6
    GENETICS 466 Principles of Genetics3
    GENETICS 468 General Genetics 23
    MICROBIO 470 Microbial Genetics & Molecular Machines3

    Intermediate/Advanced Courses

    Minimum of 13 credits required and must include one approved lab course. Approved lab courses are indicated by footnote. A course taken to meet the Foundation requirement may not also count as an Intermediate/Advanced course.

    • Complete at least two credits from either category A or B.
    • Complete at least two credits from either category C or D.
    • Complete at least two credits from an unused category (A, B, C, D or E).

    A. Cellular and Subcellular Biology

    Course List
    Code Title Credits
    AGRONOMY/​HORT 338 Plant Breeding and Biotechnology3
    AGRONOMY/​BOTANY/​HORT 339 Plant Biotechnology: Principles and Techniques I 1 4
    AGRONOMY/​BOTANY/​HORT 340 Plant Cell Culture and Genetic Engineering3
    AN SCI/​DY SCI 362 Veterinary Genetics2
    BIOCHEM 501 Introduction to Biochemistry3
    BIOCHEM 507 General Biochemistry I3
    BIOCHEM 508 General Biochemistry II3-4
    BIOCHEM/​NUTR SCI 510 Nutritional Biochemistry and Metabolism3
    BIOCHEM 551 Biochemical Methods 1 4
    BIOCHEM 570 Computational Modeling of Biological Systems3
    BIOCHEM/​M M & I 575 Biology of Viruses2
    BIOCHEM 601 Protein and Enzyme Structure and Function2
    BIOCHEM/​GENETICS/​MICROBIO 612 Prokaryotic Molecular Biology3
    BIOCHEM/​GENETICS/​MD GENET 620 Eukaryotic Molecular Biology3
    BIOCHEM/​BOTANY 621 Plant Biochemistry3
    BIOCHEM 625 Mechanisms of Action of Vitamins and Minerals2
    BIOCHEM/​PHMCOL-M/​ZOOLOGY 630 Cellular Signal Transduction Mechanisms3
    BMOLCHEM 314 Introduction to Human Biochemistry3
    BMOLCHEM 504 Human Biochemistry Laboratory 1 3
    BMOLCHEM/​MICROBIO 668 Microbiology at Atomic Resolution3
    BOTANY/​ENTOM/​PL PATH 505 Plant-Microbe Interactions: Molecular and Ecological Aspects3
    CRB/​B M E 670 Biology of Heart Disease and Regeneration3
    GENETICS 466 Principles of Genetics3
    GENETICS 467 General Genetics 13
    GENETICS 520 Neurogenetics3
    GENETICS 527 Developmental Genetics for Conservation and Regeneration3
    GENETICS/​MD GENET/​ZOOLOGY 562 Human Cytogenetics2
    MICROBIO 607 Advanced Microbial Genetics3
    MICROBIO 470 Microbial Genetics & Molecular Machines3
    MICROBIO/​SOIL SCI 523 Soil Microbiology and Biochemistry3
    MICROBIO 551 Capstone Research Project in Microbiology 1 2
    M M & I 341 Immunology3
    M M & I/​PATH-BIO 528 Immunology3
    NEURODPT/​NTP 610 Cellular and Molecular Neuroscience4
    NEURODPT/​NTP/​ZOOLOGY 616 Lab Course in Neurobiology and Behavior 1 4
    NEURODPT/​NTP 629 Molecular and Cellular Mechanisms of Memory3
    NTP 675 Special Topics (Stem Cell in Neurobiology)1-3
    NTP 675 Special Topics (Reproductive Neuroendocrinology)1-3
    NTP 675 Special Topics (Molecular Mechanisms of Brain Damage)1-3
    ONCOLOGY/​PL PATH 640 General Virology-Multiplication of Viruses3
    PHM SCI 558 Laboratory Techniques in Pharmacology and Toxicology 1 2
    ZOOLOGY 470 Introduction to Animal Development3
    ZOOLOGY/​PSYCH 523 Neurobiology3
    ZOOLOGY 555 Laboratory in Developmental Biology 1 3
    ZOOLOGY 570 Cell Biology3
    ZOOLOGY 604 Computer-based Gene and Disease/Disorder Research Lab 1 2
    ZOOLOGY 625 Development of the Nervous System2
    ZOOLOGY 655 Modeling Neurodevelopmental Disease3

    B. Organismal Biology

    Course List
    Code Title Credits
    AN SCI/​DY SCI 373 Animal Physiology3
    AN SCI/​DY SCI 434 Reproductive Physiology 1 3
    AN SCI/​F&W ECOL/​ZOOLOGY 520 Ornithology3
    AN SCI/​F&W ECOL/​ZOOLOGY 521 Birds of Southern Wisconsin 1 3
    ANAT&PHY 335 Physiology 1 5
    ANAT&PHY 337 Human Anatomy3
    ANAT&PHY 338 Human Anatomy Laboratory 1 2
    ANAT&PHY 435 Fundamentals of Human Physiology 1 5
    ANTHRO/​NTP/​PSYCH/​ZOOLOGY 619 Biology of Mind3
    BIOCORE 486 Principles of Physiology Laboratory 1 2
    BOTANY 300 Plant Anatomy 1 4
    BOTANY 330 Algae 1 3
    BOTANY/​PL PATH 332 Fungi 1 4
    BOTANY/​PL PATH 333 Biology of the Fungi2
    BOTANY/​F&W ECOL 402 Dendrology 1 2
    BOTANY 500 Plant Physiology 1 3-4
    CS&D 503 Neural Mechanisms of Speech, Hearing and Language3
    DY SCI 378 Lactation Physiology 1 3
    ENTOM/​ZOOLOGY 302 Introduction to Entomology 1 4
    ENTOM 321 Physiology of Insects3
    ENTOM 331 Taxonomy of Mature Insects 1 4
    F&W ECOL 401 Physiological Animal Ecology3
    GENETICS 545 Genetics Laboratory 1 2
    GENETICS/​MD GENET 565 Human Genetics3
    GEOSCI/​ZOOLOGY 542 Invertebrate Paleontology3
    KINES 314 Physiology of Exercise 1 4
    MICROBIO 303 Biology of Microorganisms3
    MICROBIO 304 Biology of Microorganisms Laboratory 1 2
    MICROBIO 330 Host-Parasite Interactions3
    MICROBIO 526 Physiology of Microorganisms3
    M M & I 301 Pathogenic Bacteriology2
    M M & I/​ENTOM/​PATH-BIO/​ZOOLOGY 350 Parasitology3
    M M & I 410 Medical Mycology2
    NTP/​NEURODPT/​PSYCH 611 Systems Neuroscience4
    NTP/​ZOOLOGY 620 Neuroethology Seminar2
    NTP/​NEURODPT 630 Neuronal Mechanisms for Sensation and Memory in Cerebral Cortex3
    NTP 675 Special Topics (Functional Brain Imaging of Cognitive Disorders)1-3
    NUTR SCI 431 Nutrition in the Life Span3
    NUTR SCI 631 Clinical Nutrition I3
    NUTR SCI/​PHM PRAC 672 Herbals, Homeopathy, and Dietary Supplements2-3
    ONCOLOGY 401 Introduction to Experimental Oncology2
    PATH 404 Pathophysiologic Principles of Human Diseases3
    PL PATH 558 Biology of Plant Pathogens 1 3
    PSYCH 406 Psychology of Perception3-4
    PSYCH 414 Cognitive Psychology3
    PSYCH 454 Behavioral Neuroscience3
    PSYCH 513 Hormones, Brain, and Behavior4
    PSYCH 606 Hormones and Behavior3
    ZOOLOGY 303 Aquatic Invertebrate Biology3
    ZOOLOGY 430 Comparative Anatomy of Vertebrates 1 5
    ZOOLOGY 603 Endocrinology3-4
    ZOOLOGY 611 Comparative and Evolutionary Physiology3
    ZOOLOGY 612 Comparative Physiology Laboratory 1 2

    C. Ecology

    Course List
    Code Title Credits
    AGRONOMY/​BOTANY/​SOIL SCI 370 Grassland Ecology3
    AGRONOMY/​ENTOM/​F&W ECOL/​M&ENVTOX 632 Ecotoxicology: The Chemical Players1
    AGRONOMY/​ENTOM/​F&W ECOL/​M&ENVTOX 633 Ecotoxicology: Impacts on Individuals1
    AGRONOMY/​ENTOM/​F&W ECOL/​M&ENVTOX 634 Ecotoxicology: Impacts on Populations, Communities and Ecosystems1
    BOTANY/​ZOOLOGY 450 Midwestern Ecological Issues: A Case Study Approach2
    BOTANY/​F&W ECOL 455 The Vegetation of Wisconsin 1 4
    BOTANY/​F&W ECOL/​ZOOLOGY 460 General Ecology 1 4
    BOTANY/​ENTOM/​ZOOLOGY 473 Plant-Insect Interactions3
    BOTANY/​ENVIR ST/​F&W ECOL/​ZOOLOGY 651 Conservation Biology3
    ENTOM 450 Basic and Applied Insect Ecology3
    ENTOM 451 Basic and Applied Insect Ecology Laboratory1
    ENVIR ST/​ZOOLOGY 315 Limnology-Conservation of Aquatic Resources2
    ENVIR ST/​LAND ARC 361 Wetlands Ecology3
    F&W ECOL 379 Principles of Wildlife Management3
    F&W ECOL 550 Forest Ecology3
    F&W ECOL/​LAND ARC/​ZOOLOGY 565 Principles of Landscape Ecology2
    F&W ECOL/​ZOOLOGY 660 Climate Change Ecology3
    GENETICS 528 Banking Animal Biodiversity: International Field Study in Costa Rica1
    MICROBIO/​AN SCI/​BOTANY 335 The Microbiome of Plants, Animals, and Humans3
    PL PATH 300 Introduction to Plant Pathology 1 4
    PL PATH 315 Plant Microbiomes 1 4
    ZOOLOGY 304 Marine Biology2
    ZOOLOGY 316 Laboratory for Limnology-Conservation of Aquatic Resources 1 2-3
    ZOOLOGY 504 Modeling Animal Landscapes3-5
    ZOOLOGY/​ENVIR ST 510 Ecology of Fishes3
    ZOOLOGY/​ENVIR ST 511 Ecology of Fishes Lab 1 2

    D. Evolution and Systematics

    Course List
    Code Title Credits
    ANTHRO 302 Hominoid Evolution3
    ANTHRO 304 Heredity, Environment and Human Populations3
    ANTHRO/​BOTANY/​ZOOLOGY 410 Evolutionary Biology3
    ANTHRO 411 The Evolution of the Genus, Homo3
    ANTHRO 458 Primate Behavioral Ecology3
    ANTHRO 603 Seminar in Evolutionary Theory3
    BIOLOGY/​GENETICS 522 Communicating Evolutionary Biology2-3
    BOTANY 305 Plant Morphology and Evolution 1 4
    BOTANY 400 Plant Systematics 1 4
    BOTANY 401 Vascular Flora of Wisconsin 1 4
    BOTANY 422 Plant Geography3
    BOTANY 563 Phylogenetic Analysis of Molecular Data3
    ENTOM 432 Taxonomy and Bionomics of Immature Insects 1 4
    ENTOM/​GENETICS/​ZOOLOGY 624 Molecular Ecology3
    ENVIR ST/​F&W ECOL/​ZOOLOGY 360 Extinction of Species3
    GENETICS 468 General Genetics 23
    GEOSCI/​ZOOLOGY 541 Paleobiology3
    MICROBIO 450 Diversity, Ecology and Evolution of Microorganisms3
    PSYCH 449 Animal Behavior3
    PSYCH 450 Primates and Us: Insights into Human Biology and Behavior3
    ZOOLOGY 300 Invertebrate Biology and Evolution3
    ZOOLOGY 301 Invertebrate Biology and Evolution Lab 1 2
    ZOOLOGY 425 Behavioral Ecology3

    E. Applied Biology, Agriculture and Natural Resources

    Course List
    Code Title Credits
    A A E/​AGRONOMY/​INTER-AG/​NUTR SCI 350 World Hunger and Malnutrition3
    AGRONOMY 300 Cropping Systems3
    AGRONOMY 302 Forage Management and Utilization3
    AGRONOMY/​HORT 360 Genetically Modified Crops: Science, Regulation & Controversy2
    AGRONOMY 377 Global Food Production and Health3
    AGRONOMY/​DY SCI/​INTER-AG 471 Food Production Systems and Sustainability3
    AGRONOMY/​HORT 501 Principles of Plant Breeding3
    AGRONOMY/​ATM OCN/​SOIL SCI 532 Environmental Biophysics3
    AMER IND/​ANTHRO/​BOTANY 474 Ethnobotany3-4
    AN SCI/​DY SCI/​NUTR SCI 311 Comparative Animal Nutrition3
    AN SCI/​DY SCI 320 Animal Health and Disease3
    AN SCI/​DY SCI 361 Introduction to Animal and Veterinary Genetics2
    AN SCI/​DY SCI 363 Principles of Animal Breeding2
    AN SCI 503 Avian Physiology 1 3
    AN SCI 512 Management for Avian Health 1 3
    BIOCORE 587 Biological Interactions3
    BOTANY 403 Field Collections and Identification1-4
    ENTOM 351 Principles of Economic Entomology3
    ENTOM/​ZOOLOGY 371 Medical Entomology 1 3
    ENTOM/​F&W ECOL 500 Insects in Forest Ecosystem Function and Management2
    ENVIR ST/​POP HLTH 471 Introduction to Environmental Health3
    ENVIR ST/​POP HLTH 502 Air Pollution and Human Health3
    F&W ECOL 306 Terrestrial Vertebrates: Life History and Ecology 1 4
    F&W ECOL/​HORT/​LAND ARC/​PL PATH 309 Diseases of Trees and Shrubs3
    F&W ECOL 318 Principles of Wildlife Ecology3
    F&W ECOL/​ZOOLOGY 335 Human/Animal Relationships: Biological and Philosophical Issues3
    F&W ECOL 410 Principles of Silviculture3
    F&W ECOL 415 Tree Physiology3
    F&W ECOL/​SURG SCI 548 Diseases of Wildlife3
    F&W ECOL 561 Wildlife Management Techniques 1 3
    FOOD SCI/​MICROBIO 324 Food Microbiology Laboratory 1 2
    FOOD SCI/​MICROBIO 325 Food Microbiology3
    FOOD SCI 532 Integrated Food Manufacturing 1 4
    GENETICS 548 The Genomic Revolution3
    GENETICS/​HORT 550 Molecular Approaches for Potential Crop Improvement3
    HORT/​LAND ARC 263 Landscape Plants I 1 3
    HORT 370 World Vegetable Crops3
    HORT 372 Colloquium in Organic Agriculture1
    HORT/​AGRONOMY 376 Tropical Horticultural Systems1
    HORT 378 Tropical Horticultural Systems International Field Study2
    HORT/​PATH-BIO 500 Molecular Biology Techniques 1 3
    M&ENVTOX/​ONCOLOGY/​PHM SCI/​PHMCOL-M/​POP HLTH 625 Toxicology I3
    MED PHYS/​NTP 651 Methods for Neuroimaging Research3
    MICROBIO/​SOIL SCI 425 Environmental Microbiology3
    M M & I 554 Emerging Infectious Diseases and Bioterrorism2
    NUTR SCI 332 Human Nutritional Needs3
    PL PATH/​SOIL SCI 323 Soil Biology3
    PL PATH 517 Plant Disease Resistance2-3
    SOIL SCI 321 Soils and Environmental Chemistry3
    ZOOLOGY 500 Undergraduate Neurobiology Seminar1

    Additional lab or Field Research

    In addition to the Lab requirement, complete one of the following requirements:

    • Complete one additional lab course and at least two credits from categories A–E in the Intermediate/Advanced course lists, or
    • Complete at least two credits of directed study in a biological science discipline, or
    • Complete a two-semester thesis in biological science. 2

    Approved Directed Study courses

    To have Directed Study count for the Additional Lab/Field Research requirement, students must first complete an Introductory Biology sequence.


    Watch the video: Βιολογία #4: Φυσική Επιλογή (October 2022).