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4.1: Studying Cells - Biology

4.1: Studying Cells - Biology


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Skills to Develop

  • Describe the role of cells in organisms
  • Compare and contrast light microscopy and electron microscopy
  • Summarize cell theory

A cell is the smallest unit of a living thing. Thus, cells are the basic building blocks of all organisms.

Several cells of one kind that interconnect with each other and perform a shared function form tissues, several tissues combine to form an organ (your stomach, heart, or brain), and several organs make up an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being). Here, we will examine the structure and function of cells.

There are many types of cells, all grouped into one of two broad categories: prokaryotic and eukaryotic. For example, both animal and plant cells are classified as eukaryotic cells, whereas bacterial cells are classified as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, let’s first examine how biologists study cells.

Microscopy

Cells vary in size. With few exceptions, individual cells cannot be seen with the naked eye, so scientists use microscopes (micro- = “small”; -scope = “to look at”) to study them. A microscope is an instrument that magnifies an object. Most photographs of cells are taken with a microscope, and these images can also be called micrographs.

The optics of a microscope’s lenses change the orientation of the image that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when viewed through a microscope, and vice versa. Similarly, if the slide is moved left while looking through the microscope, it will appear to move right, and if moved down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image. Because of the manner by which light travels through the lenses, this system of two lenses produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright).

Light Microscopes

To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter; the head of a pin of is about two thousandths of a meter (two mm) in diameter. That means about 250 red blood cells could fit on the head of a pin.

Most student microscopes are classified as light microscopes (Figure (PageIndex{1})a). Visible light passes and is bent through the lens system to enable the user to see the specimen. Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells.

Light microscopes commonly used in the undergraduate college laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the ability of a microscope to distinguish two adjacent structures as separate: the higher the resolution, the better the clarity and detail of the image. When oil immersion lenses are used for the study of small objects, magnification is usually increased to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes.

Electron Microscopes

In contrast to light microscopes, electron microscopes (Figure 4.1.1b) use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure (PageIndex{2})), it also provides higher resolving power. The method used to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so living cells cannot be viewed with an electron microscope.

In a scanning electron microscope, a beam of electrons moves back and forth across a cell’s surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell’s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes.

(a) (b)

Figure (PageIndex{2}): (a) These Salmonella bacteria appear as tiny purple dots when viewed with a light microscope. (b) This scanning electron microscope micrograph shows Salmonella bacteria (in red) invading human cells (yellow). Even though subfigure (b) shows a different Salmonella specimen than subfigure (a), you can still observe the comparative increase in magnification and detail. (credit a: modification of work by CDC/Armed Forces Institute of Pathology, Charles N. Farmer, Rocky Mountain Laboratories; credit b: modification of work by NIAID, NIH; scale-bar data from Matt Russell)

Link to Learning

For another perspective on cell size, try the HowBig interactive at this site.

Cell Theory

The microscopes we use today are far more complex than those used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of protista (a type of single-celled organism) and sperm, which he collectively termed “animalcules.”

In a 1665 publication called Micrographia, experimental scientist Robert Hooke coined the term “cell” for the box-like structures he observed when viewing cork tissue through a lens. In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells.

By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that all living things are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory.

Career Connection: Cytotechnologist

Have you ever heard of a medical test called a Pap smear (Figure (PageIndex{3}))? In this test, a doctor takes a small sample of cells from the uterine cervix of a patient and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection.

Cytotechnologists (cyto- = “cell”) are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal. Their focus is not limited to cervical cells; they study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, who is a medical doctor who can make a clinical diagnosis.

Cytotechnologists play a vital role in saving people’s lives. When abnormalities are discovered early, a patient’s treatment can begin sooner, which usually increases the chances of a successful outcome.

A cell is the smallest unit of life. Most cells are so tiny that they cannot be seen with the naked eye. Therefore, scientists use microscopes to study cells. Electron microscopes provide higher magnification, higher resolution, and more detail than light microscopes. The unified cell theory states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells.

cell theory
see unified cell theory
electron microscope
an instrument that magnifies an object using a beam of electrons passed and bent through a lens system to visualize a specimen
light microscope
an instrument that magnifies an object using a beam visible light passed and bent through a lens system to visualize a specimen
microscope
an instrument that magnifies an object
unified cell theory
a biological concept that states that all organisms are composed of one or more cells; the cell is the basic unit of life; and new cells arise from existing cells

MCB Major Requirements - At a Glance

The major in Molecular & Cell Biology exposes students in the fundamentals of biochemistry, molecular biology, genetics, and cell biology, and also encourages students to focus their studies in one of five undergraduate major emphases. The deadline to declare MCB is the semester before the Expected Graduation Term listed in CalCentral.

Lower Division Requirements

The lower division requirements are the same for all major emphases except Biochemistry & Molecular Biology-Track 2: Biological Chemistry (see BMB page for more info). See here for sample 4-year plans.


Gene mutation: a change to the base sequence of a gene.

Sickle cell anaemia is a genetic disease that affects red blood cells in the body. It is due to a mutation on the Hb gene which codes for a polypeptide of 146 amino acids which is part of haemoglobin (haemoglobin is an important protein component in red blood cells). In sickle cell anaemia the codon GAG found in the normal Hb gene is mutated to GTG. This is called a base substitution mutation as adenine (A) is replaced by thymine (T). This means that when the mutated gene is transcribed, a codon in the messenger RNA will be different. Instead of the normal codon GAG, the messenger RNA will contain the codon GUG. This in turn will result in a mistake during translation. In a healthy individual the codon GAG on the messenger RNA matches with the anticodon CUC on the transfer RNA carrying the amino acid glutamic acid. However, if the mutated gene is present then GUG on the messenger RNA matches with the anticodon CAC on the transfer RNA which carries the amino acid valine. So the base substitution mutation has caused glutamic acid to be replaced by valine on the sixth position on the polypeptide. This results in haemoglobin S being present in red blood cells instead of the normal haemoglobin A. This has an effect on the phenotype as instead of normal donut shaped red blood cells being produced some of the red blood cells will be sickle shaped. As a result these sickle shaped red blood cells cannot carry oxygen as efficiently as normal red blood cells would. However, there is an advantage to sickle cell anemia. The sickle cell red blood cells give resistance to malaria and so the allele Hb s on the Hb gene which causes sickle cell anemia is quite common in parts of the world where malaria is found as it provides an advantage over the disease.


Discussion

In this analysis, we present a computational approach based on overexpression of gene signatures for profiling the immune infiltration patterns in bulk tumor samples. Our methodology is different from deconvolution methods such as CIBERSORT [16] and DeconRNA-Seq [17] in that no regression or quadratic programming is involved, and only the ranks of the genes are used to infer relative cell levels. Hence, our approach does not “deconvolve” the mRNA expression data, but simply “decomposes” the immune infiltrate in the tumor microenvironment into levels of individual immune cell populations.

Compared to CIBERSORT and DeconRNA-Seq, our decomposition method has the advantages of (1) being compatible with both microarray and RNA-Seq platforms, and (2) not requiring reference expression vectors, which actually reduce the robustness of a method due to the fact that even small changes in the reference vectors may lead to substantial differences in the output when the deconvolution goal is cast into an optimization problem as in CIBERSORT and DeconRNA-Seq. Immune cell reference expression vectors are highly structured, static snapshots of the transcriptional programs of cell populations, and are highly likely to show inter-laboratory differences due to immune cells’ stimulation method, polarization state, activation state, exhaustion, or anergy. In contrast, the most abundantly expressed genes for a given cell type show little difference across different conditions. Therefore, gene signatures as in our approach offer a flexible yet principled approach to arrive at robust results.

One caveat to gene signatures is that two of them are defined by only a single gene in this study: Tregs (FOXP3) and pDCs (IL3RA). Decomposition of immune cell types with only few signatures genes is likely to be less robust than for immune cell types with many signature genes. Nevertheless, we observed that the pDC score was highly correlated with the angiogenesis score (a 40-gene signature) across many cancer types (Additional file 1: Figure S25) and this association has a known mechanism whereby pDCs induce angiogenesis [63]. Also, we were able to validate the Treg scores with immunofluorescence. Therefore, we feel confident that, despite the small number of genes, these signatures are tracking the intended cells.

Our results highlighted the immunotherapy-responsive tumors ccRCC and LUAD as having the highest T cell infiltration median. Moreover, ccRCC, but not LUAD, demonstrated significant upregulation of antigen presentation machinery in comparison with adjacent normal tissue. Preliminary evidence emerging from clinical trials of immune checkpoint blockade therapy suggests that high mutation burdens may be predictive of good responses in NSCLC and melanoma [10, 11]. However, ccRCC is another immunotherapy-responsive tumor despite bearing orders of magnitudes fewer mutations than NSCLC and melanoma. Our data suggest that ccRCC tumors may be responsive to checkpoint blockade because of a potent pre-existing immune infiltration and overall elevated level of antigen presentation and recognition.

Immune checkpoint blockade is generally thought to function by augmenting the activity of T cells subsequent to their priming by activated antigen presenting cells [64]. This suggests that “upstream” immunologic events (such as the stimulation of antigen presenting machinery) occur at baseline, resulting in primed anti-tumor T cells that are, in turn, made capable of controlling tumor growth upon treatment with immune checkpoint blockade. It is thus tempting to speculate that such events (resulting in effective antigen presentation) could be used to screen candidates for immunotherapy in the future. Our results on treatment response to the anti-PD-1 mAb nivolumab (Fig. 8) suggest the hypothesis that a pre-treatment analysis of antigen presenting machinery, and the corresponding T cell infiltrate, could be one method of achieving this. Given that PD-1 blocking mAbs are approved for a growing list of diverse cancers, such results could be applicable well beyond ccRCC.

Unsupervised clustering of ccRCC tumors using immune infiltration levels revealed three clusters of differentially infiltrated tumors, which were subsequently validated in an independent cohort. In particular, we found that the T cell enriched cluster was characterized by high expression levels of immune-response related genes including the immune checkpoint genes PD-1, PD-L1, and CTLA-4. Interestingly, a recent study also identified an aggressive, sunitinib-resistant molecular subtype of metastatic ccRCC with cellular and molecular characteristics similar to the T cell enriched tumors discovered here [65]. These findings across several cohorts of ccRCC patients suggest that a subset of ccRCC tumors may be both highly immune-infiltrated and immunosuppressed, as indicated by elevated expression of immune-checkpoint surface markers. Our findings also underscore the prognostic significance of specific T cell subsets, consistent with previous tissue-based studies of ccRCC and other tumor types [66].

Our in-depth analysis including driver mutations, CNVs, mutation burden, and neo-antigens was not able to identify any molecular mechanisms for the differential immune infiltration in ccRCC clusters. However, the lack of association between immune infiltration and predicted MHC-I binding tumor neo-antigens does not rule out neo-antigens as a driver of immune infiltration. Further, computational techniques for the prediction of immunogenic neo-antigens are not yet mature: most studies focusing on immunogenic epitopes remedy this shortcoming by using a combination of computational, biochemical, and cellular techniques. Others have suggested that the clonality of neo-antigens may drive immune recognition [59] and we consistently observed an inverse correlation between intratumor heterogeneity and immune infiltration in multiple datasets. An important caveat of the clonality analysis is that spatially segregated clones cannot be identified in the TCGA dataset. Overall, our results suggest that genetic alterations, mutation burden, and predicted neo-antigens currently provide an incomplete explanation for the degree of immune infiltration in ccRCC.

Our results illustrate the utility of ssGSEA for inferring immune infiltration levels in tumor specimens. The methodology in this study could directly be extended to the investigation of immune infiltration and its potential drivers in other tumor types and in various clinical settings including response to checkpoint blockade.


What Are Cells?

All living organisms are composed of cells. Some organisms are comprised of cells that number in the trillions. There are two primary types of cells: eukaryotic and prokaryotic cells. Eukaryotic cells have a defined nucleus, while the prokaryotic nucleus is not defined or contained within a membrane. While all organisms are composed of cells, these cells differ among organisms. Some of these differing characteristics include cell structure, size, shape, and organelle content. For example, animal cells, bacterial cells, and plant cells have similarities, but they are also noticeably different. Cells have different methods of reproduction. Some of these methods include: binary fission, mitosis, and meiosis. Cells house an organisms genetic material (DNA), which provides instructions for all cellular activity.


Illustrated report on cell biology

THANK YOU for your example , made it much clearer for me

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DATA TABLE: Cell Size Comparison

2. Calculate the total surface area for each cell model by the following formula:

surface area = (Length X Width) X 6 sides

Record the surface areas in the DATA TABLE.

3. Calculate the volumes for each cell model by the following formula:

volume = length X width X height

Record the volumes in the DATA TABLE.

4. Calculate the surface area-to-volume ratio for each cell model by the following formula:

ratio = surface area
volume

Record the ratio values in the DATA TABLE.
These ratios show how many times larger the surface area is as compared to the volume. Notice that it becomes less than one very quickly.

1. Which model has the largest surface area?

2. Which model has the largest volume?

3. Which model has the largest ratio?

4. To maintain life, and carry-out cellular functions, materials must be able to move into and out of the cell. Also, material needs to be able to move within the cell. What might be the advantage of having a large surface area?


Summary

In summary, many factors can affect mite reproduction. These range from type of reproductive host (drone, worker, or queen), cell size, age of the larvae, phoretic host type, relative humidity, or even movement of the combs. The more we understand about how reproduction is regulated in mites, the easier it will be for us to find a way that disrupts mite reproduction while not harming the bees. The trick is that the method has to be easy and economical to implement. Thus, “basic research” into the reproductive biology of mites will eventually become useful to beekeepers, as it may one day provide a new method for mite control.


As you learn more about cell organelles, you will find that they all have a membrane. Organelle membranes do not have the same chemical makeup as the cell membrane. They have different lipids and proteins that make them unique. The membrane that surrounds a lysosome is different from the membrane around the endoplasmic reticulum.

Some organelles have two membranes. A mitochondrion has an outer and inner membrane. The outer membrane contains the mitochondrion parts. The inner membrane holds digestive enzymes that break down food. While we talk about membranes all the time, you should remember they all use a basic phospholipid bilayer structure, but you will find many variations throughout the cell.


Watch the video: 18. Ανασυνδυασμένο DNA, Γονιδιωματική Βιβλιοθήκη 1 4ο κεφ. - Βιολογία Γ λυκείου (May 2022).


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