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Broadly speaking, there are two kinds of microscopy. In Light Microscopy, the specimen on the slide is viewed through optical glass lenses. In Electron Microscopy, the viewer is looking at an image on a screen created by electrons passing through, or reflected from the specimen. For a sampling of light and electron micrographs, check out this Gallery of Micrographs. Here we compare and contrast different microscopic techniques.
A. Light Microscopy
Historically one form or other of light microscopy has revealed much of what we know of cellular diversity. Check out the Drawings of Mitosisfor a reminder of how eukaryotic cells divide and then check out The Optical Microscopefor descriptions of different variations of light microscopy (e.g., bright-field, dark field, phase-contrast, fluorescence, etc.). Limits of magnification and resolution of 1200X and 2 mm, (respectively) are common to all forms of light microscopy. The main variations of light microscopy are briefly described below.
1. Bright-Field microscopy is the most common kind of light microscopy, in which the specimen is illuminated from below. Contrast between regions of the specimen comes from the difference between light absorbed by the sample and light passing through it. Live specimens lack contrast in conventional bright-field microscopy because differences in refractive index between components of the specimen (e.g., organelles and cytoplasm in cells) diffuse the resolution of the magnified image. This is why Bright-Field microscopy is best suited to fixed and stained specimens.
2. In Dark-field illumination, light passing through the center of the specimen is blocked and the light passing through the periphery of the beam is diffracted (“scattered”) by the sample. The result is enhanced contrast for certain kinds of specimens, including live, unfixed and unstained ones.
3. In Polarized light microscopy, light is polarized before passing through the specimen, allowing the investigator to achieve the highest contrast by rotating the plane of polarized light passing through the sample. Samples can be unfixed, unstained or even live.
4. Phase-Contrast or Interference microscopy enhances contrast between parts of a specimen with higher refractive indices (e.g., cell organelles) and lower refractive indices (e.g., cytoplasm). Phase–Contrast microscopy optics shift the phase of the light entering the specimen from below by a half a wavelength to capture small differences in refractive index and thereby increase contrast. Phase–Contrast microscopy is a most cost-effective tool for examining live, unfixed and unstained specimens.
5. In a fluorescence microscope, short wavelength, high-energy (usually UV) light is passed through a specimen that has been treated with a fluorescing chemical covalently attached to other molecules (e.g., antibodies) that fluoresces when struck by the light source. This fluorescent tag was chosen to recognize and bind specific molecules or structures in a cell. Thus, in fluorescence microscopy, the visible color of fluorescence marks the location of the target molecule/structure in the cell.
6. Confocal microscopy is a variant of fluorescence microscopy that enables imaging through thick samples and sections. The result is often 3D-like, with much greater depth of focus than other light microscope methods. Click at Gallery of Confocal Microscopy Imagesto see a variety of confocal micrographs and related images; look mainly at the specimens.
7. Lattice Light-Sheet Microscopy is a 100 year old variant of light microscopy that allows us to follow subcellular structures and macromolecules moving about in living cells. It was recently applied to follow the movement and sub-cellular cellular location of RNA molecules associated with proteins in structures called RNA granules (check it out at RNA Organization in a New Light).
B. Electron Microscopy
Unlike light (optical) microscopy, electron microscopy generates an image by passing electrons through, or reflecting electrons from a specimen, and capturing the electron image on a screen. Transmission Electron Microscopy (TEM) can achieve much higher magnification (up to 106X) and resolution (2.0 nm) than any form of optical microscopy! Scanning Electron Microscopy (SEM) can magnify up to 105X with a resolution of 3.0-20.0 nm. TEM, together with biochemical and molecular biological studies, continues to reveal how different cell components work with each other. The higher voltage in High Voltage Electron microscopy is an adaptation that allows TEM through thicker sections than regular (low voltage) TEM. The result is micrographs with greater resolution, depth and contrast. SEM allows us to examine the surfaces of tissues, small organisms like insects, and even of cells and organelles. Check this link to Scanning Electron Microscopyfor a description of scanning EM, and look at the gallery of SEM images at the end of the entry.
121 Electron Microscopy
1.1 The Science of Biology
By the end of this section, you will be able to do the following:
- Identify the shared characteristics of the natural sciences
- Summarize the steps of the scientific method
- Compare inductive reasoning with deductive reasoning
- Describe the goals of basic science and applied science
What is biology? In simple terms, biology is the study of life. This is a very broad definition because the scope of biology is vast. Biologists may study anything from the microscopic or submicroscopic view of a cell to ecosystems and the whole living planet (Figure 1.2). Listening to the daily news, you will quickly realize how many aspects of biology we discuss every day. For example, recent news topics include Escherichia coli (Figure 1.3) outbreaks in spinach and Salmonella contamination in peanut butter. Other subjects include efforts toward finding a cure for AIDS, Alzheimer’s disease, and cancer. On a global scale, many researchers are committed to finding ways to protect the planet, solve environmental issues, and reduce the effects of climate change. All of these diverse endeavors are related to different facets of the discipline of biology.
The Process of Science
Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? We can define science (from the Latin scientia, meaning “knowledge”) as knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific method. It becomes clear from this definition that applying scientific method plays a major role in science. The scientific method is a method of research with defined steps that include experiments and careful observation.
We will examine scientific method steps in detail later, but one of the most important aspects of this method is the testing of hypotheses by means of repeatable experiments. A hypothesis is a suggested explanation for an event, which one can test. Although using the scientific method is inherent to science, it is inadequate in determining what science is. This is because it is relatively easy to apply the scientific method to disciplines such as physics and chemistry, but when it comes to disciplines like archaeology, psychology, and geology, the scientific method becomes less applicable as repeating experiments becomes more difficult.
These areas of study are still sciences, however. Consider archaeology—even though one cannot perform repeatable experiments, hypotheses may still be supported. For instance, an archaeologist can hypothesize that an ancient culture existed based on finding a piece of pottery. He or she could make further hypotheses about various characteristics of this culture, which could be correct or false through continued support or contradictions from other findings. A hypothesis may become a verified theory. A theory is a tested and confirmed explanation for observations or phenomena. Therefore, we may be better off to define science as fields of study that attempt to comprehend the nature of the universe.
What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain functions? A planetarium? Gems and minerals? Maybe all of the above? Science includes such diverse fields as astronomy, biology, computer sciences, geology, logic, physics, chemistry, and mathematics (Figure 1.4). However, scientists consider those fields of science related to the physical world and its phenomena and processes natural sciences . Thus, a museum of natural sciences might contain any of the items listed above.
There is no complete agreement when it comes to defining what the natural sciences include, however. For some experts, the natural sciences are astronomy, biology, chemistry, earth science, and physics. Other scholars choose to divide natural sciences into life sciences , which study living things and include biology, and physical sciences , which study nonliving matter and include astronomy, geology, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on both life and physical sciences and are interdisciplinary. Some refer to natural sciences as “hard science” because they rely on the use of quantitative data. Social sciences that study society and human behavior are more likely to use qualitative assessments to drive investigations and findings.
Not surprisingly, the natural science of biology has many branches or subdisciplines. Cell biologists study cell structure and function, while biologists who study anatomy investigate the structure of an entire organism. Those biologists studying physiology, however, focus on the internal functioning of an organism. Some areas of biology focus on only particular types of living things. For example, botanists explore plants, while zoologists specialize in animals.
One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the development of science. Scientists seek to understand the world and the way it operates. To do this, they use two methods of logical thinking: inductive reasoning and deductive reasoning.
Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data can be qualitative or quantitative, and one can supplement the raw data with drawings, pictures, photos, or videos. From many observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating generalizations inferred from careful observation and analyzing a large amount of data. Brain studies provide an example. In this type of research, scientists observe many live brains while people are engaged in a specific activity, such as viewing images of food. The scientist then predicts the part of the brain that “lights up” during this activity to be the part controlling the response to the selected stimulus, in this case, images of food. Excess absorption of radioactive sugar derivatives by active areas of the brain causes the various areas to "light up". Scientists use a scanner to observe the resultant increase in radioactivity. Then, researchers can stimulate that part of the brain to see if similar responses result.
Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reasoning, the pattern of thinking moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a general principle or law to predict specific results. From those general principles, a scientist can deduce and predict the specific results that would be valid as long as the general principles are valid. Studies in climate change can illustrate this type of reasoning. For example, scientists may predict that if the climate becomes warmer in a particular region, then the distribution of plants and animals should change.
Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based science. Descriptive (or discovery) science , which is usually inductive, aims to observe, explore, and discover, while hypothesis-based science , which is usually deductive, begins with a specific question or problem and a potential answer or solution that one can test. The boundary between these two forms of study is often blurred, and most scientific endeavors combine both approaches. The fuzzy boundary becomes apparent when thinking about how easily observation can lead to specific questions. For example, a gentleman in the 1940s observed that the burr seeds that stuck to his clothes and his dog’s fur had a tiny hook structure. On closer inspection, he discovered that the burrs’ gripping device was more reliable than a zipper. He eventually experimented to find the best material that acted similarly, and produced the hook-and-loop fastener popularly known today as Velcro. Descriptive science and hypothesis-based science are in continuous dialogue.
The Scientific Method
Biologists study the living world by posing questions about it and seeking science-based responses. Known as scientific method, this approach is common to other sciences as well. The scientific method was used even in ancient times, but England’s Sir Francis Bacon (1561–1626) first documented it (Figure 1.5). He set up inductive methods for scientific inquiry. The scientific method is not used only by biologists researchers from almost all fields of study can apply it as a logical, rational problem-solving method.
The scientific process typically starts with an observation (often a problem to solve) that leads to a question. Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem: the classroom is too warm. The student then asks a question: “Why is the classroom so warm?”
Proposing a Hypothesis
Recall that a hypothesis is a suggested explanation that one can test. To solve a problem, one can propose several hypotheses. For example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” However, there could be other responses to the question, and therefore one may propose other hypotheses. A second hypothesis might be, “The classroom is warm because there is a power failure, and so the air conditioning doesn’t work.”
Once one has selected a hypothesis, the student can make a prediction. A prediction is similar to a hypothesis but it typically has the format “If . . . then . . . .” For example, the prediction for the first hypothesis might be, “If the student turns on the air conditioning, then the classroom will no longer be too warm.”
Testing a Hypothesis
A valid hypothesis must be testable. It should also be falsifiable , meaning that experimental results can disprove it. Importantly, science does not claim to “prove” anything because scientific understandings are always subject to modification with further information. This step—openness to disproving ideas—is what distinguishes sciences from non-sciences. The presence of the supernatural, for instance, is neither testable nor falsifiable. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the hypotheses. Each experiment will have one or more variables and one or more controls. A variable is any part of the experiment that can vary or change during the experiment. The control group contains every feature of the experimental group except it is not given the manipulation that the researcher hypothesizes. Therefore, if the experimental group's results differ from the control group, the difference must be due to the hypothesized manipulation, rather than some outside factor. Look for the variables and controls in the examples that follow. To test the first hypothesis, the student would find out if the air conditioning is on. If the air conditioning is turned on but does not work, there should be another reason, and the student should reject this hypothesis. To test the second hypothesis, the student could check if the lights in the classroom are functional. If so, there is no power failure and the student should reject this hypothesis. The students should test each hypothesis by carrying out appropriate experiments. Be aware that rejecting one hypothesis does not determine whether or not one can accept the other hypotheses. It simply eliminates one hypothesis that is not valid (Figure 1.6). Using the scientific method, the student rejects the hypotheses that are inconsistent with experimental data.
While this “warm classroom” example is based on observational results, other hypotheses and experiments might have clearer controls. For instance, a student might attend class on Monday and realize she had difficulty concentrating on the lecture. One observation to explain this occurrence might be, “When I eat breakfast before class, I am better able to pay attention.” The student could then design an experiment with a control to test this hypothesis.
In hypothesis-based science, researchers predict specific results from a general premise. We call this type of reasoning deductive reasoning: deduction proceeds from the general to the particular. However, the reverse of the process is also possible: sometimes, scientists reach a general conclusion from a number of specific observations. We call this type of reasoning inductive reasoning, and it proceeds from the particular to the general. Researchers often use inductive and deductive reasoning in tandem to advance scientific knowledge (Figure 1.7). In recent years a new approach of testing hypotheses has developed as a result of an exponential growth of data deposited in various databases. Using computer algorithms and statistical analyses of data in databases, a new field of so-called "data research" (also referred to as "in silico" research) provides new methods of data analyses and their interpretation. This will increase the demand for specialists in both biology and computer science, a promising career opportunity.
In the example below, the scientific method is used to solve an everyday problem. Match the scientific method steps (numbered items) with the process of solving the everyday problem (lettered items). Based on the results of the experiment, is the hypothesis correct? If it is incorrect, propose some alternative hypotheses.
|1. Observation||a. There is something wrong with the electrical outlet.|
|2. Question||b. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.|
|3. Hypothesis (answer)||c. My toaster doesn’t toast my bread.|
|4. Prediction||d. I plug my coffee maker into the outlet.|
|5. Experiment||e. My coffeemaker works.|
|6. Result||f. Why doesn’t my toaster work?|
Decide if each of the following is an example of inductive or deductive reasoning.
- All flying birds and insects have wings. Birds and insects flap their wings as they move through the air. Therefore, wings enable flight.
- Insects generally survive mild winters better than harsh ones. Therefore, insect pests will become more problematic if global temperatures increase.
- Chromosomes, the carriers of DNA, are distributed evenly between the daughter cells during cell division. Therefore, each daughter cell will have the same chromosome set as the mother cell.
- Animals as diverse as humans, insects, and wolves all exhibit social behavior. Therefore, social behavior must have an evolutionary advantage.
The scientific method may seem too rigid and structured. It is important to keep in mind that, although scientists often follow this sequence, there is flexibility. Sometimes an experiment leads to conclusions that favor a change in approach. Often, an experiment brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion. Instead, scientists continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests. Notice, too, that we can apply the scientific method to solving problems that aren’t necessarily scientific in nature.
Two Types of Science: Basic Science and Applied Science
The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to solving a specific problem or to bettering our lives? This question focuses on the differences between two types of science: basic science and applied science.
Basic science or “pure” science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is knowledge for knowledge’s sake, although this does not mean that, in the end, it may not result in a practical application.
In contrast, applied science or “technology,” aims to use science to solve real-world problems, making it possible, for example, to improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster (Figure 1.8). In applied science, the problem is usually defined for the researcher.
Some individuals may perceive applied science as “useful” and basic science as “useless.” A question these people might pose to a scientist advocating knowledge acquisition would be, “What for?” However, a careful look at the history of science reveals that basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of science is necessary before researchers develop an application, therefore, applied science relies on the results that researchers generate through basic science. Other scientists think that it is time to move on from basic science in order to find solutions to actual problems. Both approaches are valid. It is true that there are problems that demand immediate attention however, scientists would find few solutions without the help of the wide knowledge foundation that basic science generates.
One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA structure led to an understanding of the molecular mechanisms governing DNA replication. DNA strands, unique in every human, are in our cells, where they provide the instructions necessary for life. When DNA replicates, it produces new copies of itself, shortly before a cell divides. Understanding DNA replication mechanisms enabled scientists to develop laboratory techniques that researchers now use to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine paternity. Without basic science, it is unlikely that applied science could exist.
Another example of the link between basic and applied research is the Human Genome Project, a study in which researchers analyzed and mapped each human chromosome to determine the precise sequence of DNA subunits and each gene's exact location. (The gene is the basic unit of heredity represented by a specific DNA segment that codes for a functional molecule. An individual’s complete collection of genes is his or her genome.) Researchers have studied other less complex organisms as part of this project in order to gain a better understanding of human chromosomes. The Human Genome Project (Figure 1.9) relied on basic research with simple organisms and, later, with the human genome. An important end goal eventually became using the data for applied research, seeking cures and early diagnoses for genetically related diseases.
While scientists usually carefully plan research efforts in both basic science and applied science, note that some discoveries are made by serendipity , that is, by means of a fortunate accident or a lucky surprise. Scottish biologist Alexander Fleming discovered penicillin when he accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew on the dish, killing the bacteria. Fleming's curiosity to investigate the reason behind the bacterial death, followed by his experiments, led to the discovery of the antibiotic penicillin, which is produced by the fungus Penicillium. Even in the highly organized world of science, luck—when combined with an observant, curious mind—can lead to unexpected breakthroughs.
Reporting Scientific Work
Whether scientific research is basic science or applied science, scientists must share their findings in order for other researchers to expand and build upon their discoveries. Collaboration with other scientists—when planning, conducting, and analyzing results—is important for scientific research. For this reason, important aspects of a scientist’s work are communicating with peers and disseminating results to peers. Scientists can share results by presenting them at a scientific meeting or conference, but this approach can reach only the select few who are present. Instead, most scientists present their results in peer-reviewed manuscripts that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that a scientist’s colleagues or peers review. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research in a scientific paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or different conditions to expand on the findings.
A scientific paper is very different from creative writing. Although creativity is required to design experiments, there are fixed guidelines when it comes to presenting scientific results. First, scientific writing must be brief, concise, and accurate. A scientific paper needs to be succinct but detailed enough to allow peers to reproduce the experiments.
The scientific paper consists of several specific sections—introduction, materials and methods, results, and discussion. This structure is sometimes called the “IMRaD” format. There are usually acknowledgment and reference sections as well as an abstract (a concise summary) at the beginning of the paper. There might be additional sections depending on the type of paper and the journal where it will be published. For example, some review papers require an outline.
The introduction starts with brief, but broad, background information about what is known in the field. A good introduction also gives the rationale of the work. It justifies the work carried out and also briefly mentions the end of the paper, where the researcher will present the hypothesis or research question driving the research. The introduction refers to the published scientific work of others and therefore requires citations following the style of the journal. Using the work or ideas of others without proper citation is plagiarism .
The materials and methods section includes a complete and accurate description of the substances the researchers use, and the method and techniques they use to gather data. The description should be thorough enough to allow another researcher to repeat the experiment and obtain similar results, but it does not have to be verbose. This section will also include information on how the researchers made measurements and the types of calculations and statistical analyses they used to examine raw data. Although the materials and methods section gives an accurate description of the experiments, it does not discuss them.
Some journals require a results section followed by a discussion section, but it is more common to combine both. If the journal does not allow combining both sections, the results section simply narrates the findings without any further interpretation. The researchers present results with tables or graphs, but they do not present duplicate information. In the discussion section, the researchers will interpret the results, describe how variables may be related, and attempt to explain the observations. It is indispensable to conduct an extensive literature search to put the results in the context of previously published scientific research. Therefore, researchers include proper citations in this section as well.
Finally, the conclusion section summarizes the importance of the experimental findings. While the scientific paper almost certainly answers one or more scientific questions that the researchers stated, any good research should lead to more questions. Therefore, a well-done scientific paper allows the researchers and others to continue and expand on the findings.
Review articles do not follow the IMRAD format because they do not present original scientific findings, or primary literature. Instead, they summarize and comment on findings that were published as primary literature and typically include extensive reference sections.
There is increasing evidence that pathogens can play a significant role in species decline (Bunbury et al. 2007). Haemosporidian parasites, including Plasmodium, known as avian malaria, and related malaria-like pathogens Leucocytozoon and subgenera Haemoproteus and Parahaemoproteus have been associated to negatively affect bird population dynamics (Yanga et al. 2011 Yoshimura et al. 2014). Several studies demonstrated different costs on life-history traits associated with haemosporidian infections, such as impairment on the body condition (Valkiūnas et al. 2006), reduced reproductive success (Merino et al. 2000 Marzal et al. 2005 Knowles et al. 2010) and lower chance of survival (Earle et al. 1993 Sol et al. 2003 Bunbury et al. 2007 Lachish et al. 2011).
Haemosporidian parasites are widespread and infect a great variety of avian host species (Valkiūnas 2005 Boundenga et al. 2017). Nevertheless, most studies have specifically addressed avian haemosporidians of passerine birds, while research on non-passerine host species is underrepresented (Santiago-Alarcon et al. 2010 Clark et al. 2014). There is only a small number of recent publications dealing with haemosporidian parasites in wild columbiform birds, particularly in Europe, apart from feral pigeon Columba livia domestica (e.g. Sol et al. 2003 Foronda et al. 2004 Scaglione et al. 2015).
In general, given their common evolutionary background, closely related host species (i.e. species belonging to the same family) are expected to be similar in their susceptibility to parasitic infestations and exposure to vectoring dipterans and their parasite community (Ricklefs and Fallon 2002 Dubiec et al. 2016 Ciloglu et al. 2020a Ellis et al. 2020). However, only few studies have presented data on the prevalence and diversity of haemosporidian parasites in closely related bird species. Differences in prevalence between species are associated with several factors and the interactions between those, including life-history traits and ecology of the hosts and vectors, parasite characteristics and environmental conditions, that may affect the activity of vectors and the development of parasites (Sol et al. 2000 Gupta et al. 2011 Quillfeldt et al. 2011 Hellard et al. 2016 Chakarov et al. 2020 Ciloglu et al. 2020b Ellis et al. 2020). Also different behavioural characteristics (e.g. cavity-nesting vs. open-nesting or migrant vs. resident species) may influence haemosporidian prevalence and community (Dunn et al. 2017 Emmenegger et al. 2018), whereas no evidence that closely related host species share parasites due to overlapping geographic ranges was found (Ciloglu et al. 2020a). Cavity-nesting species may be shielded from vector exposure due to their enclosed surroundings, while open-nesting birds should be more susceptible to flying dipteran vectors. Migratory species, particularly long-distance migrants, are expected to host a higher diversity of parasites (Walther et al. 2016 Emmenegger et al. 2018 Ciloglu et al. 2020b) as they encounter parasites and their vectors in multiple ecosystems each year, whereas residents only encounter parasites in one ecosystem (Møller and Erriyzøe 1998). The European turtle dove Streptopelia turtur (henceforth turtle dove) is the only long-distance migrant among the columbiform birds we tested. The European population follows three main migration flyways (western, central and eastern) between Europe and sub-Saharan Africa (Marx et al. 2016). The population trend of turtle doves across Europe declined by almost 80% since the 1970s, whereas population trends of other columbiform species, like Common woodpigeon C. palumbus (henceforth woodpigeon) and stock dove C. oenas, are increasing (PECBMS 2020). Stock doves and woodpigeons from Central Europe are partial migrants. Migratory individuals are mainly wintering in France and Iberia (Cramp 1985 von Blotzheim and Bauer 1994). The main reasons for the turtle dove population decline are the loss of good-quality habitats as well as illegal and unsustainable legal hunting. Additional threats were identified, but these are either considered to have a small or unknown impact or need further research (Fisher et al. 2018) among these are diseases like haemosporidian infections.
We used molecular and microscopic techniques to screen the columbiform species for haemosporidian infections and to identify genetic lineages in order to test the following hypotheses: (i) the prevalence of haemosporidian parasites is higher in long-distance compared to short-distance migratory or resident species, (ii) the diversity of lineages differs among related species and (iii) the prevalence and lineage occurrence in turtle doves varies across their flyways due to possible differing parasite-vector-communities at different breeding, stopover and wintering areas.
Adipose tissue is perhaps the most structurally dynamic tissue in the adult human body. Its capacity to grow and shrink in size by large magnitudes is fundamental to human metabolism, health, fitness, and adaptation. Unraveling the mechanisms of this process has become increasingly important because of the growing obesity epidemic, afflicting more than 40% of the adult U.S. population and an increasing fraction of the worldwide population, including countries at all levels of development (41). Tissue microenvironments and macrophage cells are believed to be essential to adipose dynamics, with CLSs believed to be the histopathological inflammatory connection to obesity comorbidities, including metabolic disorders, glucose intolerance, and cardiovascular events (9). The counterintuitive necessity to pare and kill off cells to grow tissue in the obese state is not yet fully understood, partly because of our incomplete ability to correlate microscopic tissue structures with global tissue metabolism. Our current understanding has been limited to analyses from 2D adipose tissue sections with limited 3D structural information, and nonlinear changes have been observed in the progressive development of obesity (42). 3D analysis is needed to accurately assess CLS features such as cell composition, size, and shape, while rare events such as large CLS structures may not be possible to identify in 2D datasets. Whether these additional features will further improve correlation with clinical conditions or predict progression to comorbidities will be the focus of further studies. Time course microscopy in living tissues has revealed important dynamic processes in adipose tissues (43) however, there are considerable limitations to these techniques, as the spatial depth of confocal imaging only allows observations at the tissue periphery and with low throughput. Tissue clearing and deep learning–based image processing instead provide the capacity to comprehensively map all CLS structures and to further evaluate cell-cell interactions with much richer detail, albeit without the capacity for longitudinal analysis of individual structures (15, 44). Further studies will be needed to analyze cell subclassifications involved, as single-cell sequencing in lean and obese adipose tissues revealed seven distinct subclasses of macrophages (45). Adipocytes, while not directly probed in this work, can also be evaluated using related image analysis workflows, which may yield further insights into factors modulating organism-level metabolism, such as adipokines (e.g., adiponectin and leptin) or free fatty acids. Advanced forms of multiplexed immunolabeling, potentially applying technologies like quantum dots, will be necessary to identify numerous additional cell types and phenotype markers in heterogeneous tissue microenvironments (46) to help understand their spatial relationships, contributions to pathologies, and response to interventions. These workflows may similarly contribute to the development of novel bioengineering technologies in adipose tissue, which is a common source of stem cells, a target for novel biopharmaceuticals, and a potential depot for drug delivery (47, 48). While applications in the sciences are clear, there are still challenges that prevent the use of 3D imaging techniques in the clinic for histopathological analyses, such as long immunolabeling times and low-throughput analysis methods for terabyte-sized data (44). Deep learning in the most recent 10 years has led to streamlined procedures for image processing and analysis, with particularly impactful contributions for object recognition and localization, processes that have traditionally been manual bottlenecks in image analysis. Nevertheless, the coordinated development of tissue clearing and labeling approaches, microscopy modalities, and advanced deep learning algorithms can together drive solutions to the challenges in 3D structural biology of tissue.
Technology Aids in Important Discovery
One enzyme that&rsquos crucial to the assembly of Hedgehog proteins is known as Hedgehog acetyltransferase, or HHAT. It acts like a machine on an assembly line to link two components together and form the final Hedgehog product. Once HHAT completes this assembly step, the finished Hedgehog protein acts as a messenger. For this reason, inhibitors of HHAT, which prevent it from completing its assembly, could potentially be useful for the treatment of certain cancers that depend on Hedgehog messages.
MSK scientists are able to probe the shapes of proteins more completely than ever before thanks to an advanced imaging technology called cryogenic electron microscopy (cryo-EM), which MSK acquired in 2016.
Older methods of looking at proteins&rsquo structures, such as X-ray crystallography, require molecules to be crystallized in a repeating array, similar to a salt crystal. This can limit the ability to study proteins that are flexible. For the HHAT enzyme, it&rsquos particularly challenging because the protein is normally embedded within a membrane inside a cell.
&ldquoMembrane proteins are generally more difficult to study in the laboratory than other types of proteins, and, consequently, we know less about how they work,&rdquo Dr. Long says. Because cryo-EM doesn&rsquot require proteins to be crystallized, researchers can now decipher what the proteins look like more easily.
A Review of All Cell Organelles Through Q&As
Viruses are considered the only living organisms that do not have cells. Viruses are made up of genetic material (DNA or RNA) enclosed in a protein capsule. They do not have membranes, cell organelles, or own metabolism.
3. In 1665, Robert Hooke, an English scientist, published his book Micrographia, in which he described that pieces of cork viewed under a microscope presented small cavities, similar to pores and filled with air. Based on knowledge discovered later on, what do you think those cavities were composed of? What is the historical importance of this observation?
The walls of the cavities observed by Hooke were the walls of the plant cells that form the tissue. This observation led to the discovery of cells, a fact only possible after the invention of the microscope. In that book, Hooke established the term “cell", which is now widely used in biology, to designate those cavities seen under the microscope.
Eukaryotic and Prokaryotic Cells
4. What are the two main groups into which cells are classified?
Cells can be classified as eukaryotic or prokaryotic.
Prokaryotic cells are those that do not have an enclosed nucleus. Eukaryotic cells are those with a nucleus enclosed by a membrane.
5. Do the cells of bacteria have a nucleus?
In bacteria, genetic material is contained in the cytosol and there is no internal membrane that encloses a nucleus.
6. Are any bacteria made of more than one cell?
There are no pluricellular bacteria. All bacteria are unicellular and prokaryotic.
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7. What is the plasma membrane of the cell? What are its main functions?
The plasma membrane is the outer membrane of a cell, it encloses the cell itself, maintaining specific conditions for cellular function within the cell. Since it is selectively permeable, the plasma membrane plays an important role in the entrance and exit of substances.
8. What chemical substances compose the plasma membrane?
The main components of the plasma membrane are phospholipids, proteins and carbohydrates. Phospholipids are amphipathic molecules that are regularly organized in the membrane according to their polarity: two layers of phospholipids form the lipid bilayer, with the polar part of the phospholipids pointing to the exterior part of the layer and the non-polar phospholipid chains toward the interior. Proteins can be found embedded in the lipid bilayer. In addition, there are also some carbohydrates bound to proteins and to phospholipids in the outer surface of the membrane.
9. What is the difference between a plasma membrane and a cell wall?
A plasma membrane and a cell wall are not the same thing. The plasma membrane, also called the cell membrane, is the outer membrane common to all living cells, made of a phospholipid bilayer, embedded proteins and some bound carbohydrates.
Because cell membranes are fragile, in some types of cells, there are also external structures to support and protect the membrane, like the cellulose wall of plant cells and the chitin wall of some fungi cells. Most bacteria also have an outer cell wall made of peptidoglycans and other organic substances.
Cell Structure Review - Image Diversity: cell wall
10. What are the main respective components of cell walls in bacteria, protists, fungi and plants?
In bacteria, the cell wall is made of peptidoglycans among protists, algae have cell walls made of cellulose in fungi, the cell wall is made of chitin (the same substance that makes the exoskeleton of arthropods) and in plants, the cell wall is also made of cellulose.
11. Are membranes only present as the outside of cells?
Lipid membranes do not only form the outer layer of cells. Cell organelles, such as the Golgi complex, mitochondria, chloroplasts, lysosomes, the endoplasmic reticula and the nucleus, are also enclosed by membranes.
Cell Structure Review - Image Diversity: cell nucleus
12. Which type of cell evolved first, the eukaryotic cell or the prokaryotic cell?
This is an interesting problem of biological evolution. The most accepted hypothesis claims that the simpler cell, the prokaryotic cell, appeared earlier in evolution than the more complex eukaryotic cell. The endosymbiotic hypothesis, for example, claims that aerobic eukaryotic cells appeared from the mutualistic ecological interaction between aerobic prokaryotes and primitive anaerobic eukaryotes.
13. Regarding the presence of the nucleus, what is the difference between animal and bacterial cells?
Animal cells (the cells of organisms of the kingdom Animalia) have an interior membrane that encloses a cell nucleus and are therefore eukaryotic cells. In these cells, the genetic material is located within the nucleus. Bacterial cells (the cells of living organisms of the kingdom Monera) do not have organized cellular nuclei and are therefore prokaryotic cells. Their genetic material is found in the cytosol.
14. What are the three main parts of a eukaryotic cell?
Eukaryotic cells can be divided into three main parts: the cell membrane that physically separates the intracellular space from the outer space by enclosing the cell the cytoplasm, the interior portion filled with cytosol (the aqueous fluid inside the cell) and the nucleus, the membrane-enclosed internal region that contains genetic material.
15. What are the main structures within the nucleus of a cell?
Within the nucleus of a cell, the main structures are: the nucleolus, an optically dense region, sphere shaped region, which contains concentrated ribosomal RNA (rRNA) bound to proteins (there may be more than one nucleolus in a nucleus) the chromatin, made of DNA molecules released into the nuclear matrix during cell interphase and the karyotheca, or nuclear membrane, which is the membrane that encloses the nucleus.
16. What substances is chromatin made up of? What is the difference between chromatin and a chromosome?
Chromatin, dispersed in the nucleus, is a set of filamentous DNA molecules attached to nuclear proteins called histones. Each DNA filament is a double helix of DNA and therefore a chromosome.
17. What is the fluid that fills the nucleus called?
The aqueous fluid that fills the nuclear region is called karyolymph, or the nucleoplasm. This fluid contains proteins, enzymes and other important substances for nuclear metabolism.
18. What substances make up the nucleolus? Is there a membrane around the nucleolus?
The nucleolus is a region within the nucleus made of ribosomal RNA (rRNA) and proteins. It is not enclosed by a membrane.
19. What is the name of the membrane that encloses the nucleus? Which component of cell structure is contiguous to this membrane?
The nuclear membrane is also called the karyotheca. The nuclear membrane is contiguous to the endoplasmic reticulum membrane.
20. What are the main structures of the cytoplasm present in animal cells?
The main structures of the cytoplasm of a cell are centrioles, the cytoskeleton, lysosomes, mitochondria, peroxisomes, the Golgi apparatus, the endoplasmic reticula and ribosomes.
21. What are cytoplasmic inclusions?
Cytoplasmic inclusions are foreign molecules added to the cytoplasm, such as pigments, organic polymers and crystals. They are not considered cell organelles.
Fat droplets and glycogen granules are examples of cytoplasmic inclusions.
22. Where in the cell can ribosomes be found? What is the main biological function of ribosomes?
Ribosomes can be found unbound in the cytoplasm, attached to the outer side of the nuclear membrane or attached to the endoplasmic reticulum membrane that encloses the rough endoplasmic reticulum. Ribosomes are the structures in which protein synthesis takes place.
The Endoplasmic Reticulum
23. What is the difference between the smooth and rough endoplasmic reticulum?
The endoplasmic reticulum is a delicate membrane structure that is contiguous to the nuclear membrane and which is present in the cytoplasm. It forms an extensive net of channels throughout the cell and is classified into rough or smooth types.
The rough endoplasmic reticulum has a large number of ribosomes attached to the external side of its membrane. The smooth endoplasmic reticulum does not have ribosomes attached to its membrane.
The main functions of the rough endoplasmic reticulum are the synthesis and storage of proteins made in the ribosomes. The smooth endoplasmic reticulum plays a role in lipid synthesis and, in muscle cells, it is important in carrying out of contraction stimuli.
The Golgi Apparatus
24. A netlike membrane complex of superposed flat saccules with vesicles detaching from its extremities seen is observed during electron microscopy. What is the observed structure called? What is its biological function?
What is being observed is the Golgi complex, or Golgi apparatus. This cytoplasmic organelle is associated with chemical processing and the modification of proteins made by the cell as well as with the storage and marking of these proteins for later use or secretion. Vesicles seen under an electronic microscope contain materials already processed, ਊnd which are ready to be exported (secreted) by the cell. The vesicles detach from the Golgi apparatus, travel across the cytoplasm and fuse with the plasma membrane, secreting their substances to the exterior.
Lysosomes and Peroxysomes
25. Which organelle of the cell structure is responsible for intracellular digestion? What is the chemical content of those organelles?
Intracellular digestion occurs through the action of lysosomes. Lysosomes contain digestive enzymes (hydrolases) that are produced in the rough endoplasmic reticulum and stored in the Golgi apparatus. Lysosomes are hydrolase-containing vesicles that detach from the Golgi apparatus.
26. Why are lysosomes known as “the cleaners” of cell waste?
Lysosomes carry out autophagic and heterophagic digestion. Autophagic digestion occurs when residual substances of the cellular metabolism are digested. Heterophagic digestion takes place when substances that enter the cell are digested. Lysosomes enfold the substances to be broken down, forming digestive vacuoles or residual vacuoles, which later migrate toward the plasma membrane, fusing with it and releasing (exocytosis) the digested material to the exterior.
27. What are the morphological, chemical and functional similarities and differences between lysosomes and peroxisomes?
Similarities: lysosomes and peroxisomes are small membranous vesicles that contain enzymes and enclose residual substances of an internal or external origin to break them down. Differences: lysosomes have digestive enzymes (hydrolases) that break down substances to be digested into smaller molecules whereas peroxisomes contain enzymes that mainly break down long-chain fatty acids and amino acids, and which inactivate toxic agents including ethanol. In addition, within peroxisomes, the enzyme catalase is present. It is responsible for the oxidation of organic compounds by hydrogen peroxide (H₂O₂) and, when this substance is present in excess, it is responsible for the breaking down of the peroxide into water and molecular oxygen.
28. Which cell organelles participate in cell division and in the formation of the cilia and flagella of some eukaryotic cells?
The organelles that participate in cell division and in the formation of the cilia and flagella of some eukaryotic cells are centrioles. Some cells have cilia (paramecium, the bronchial ciliated epithelium, etc.) or flagella (flagellate protists, sperm cells, etc.). These cell structures are composed of microtubules that originate from the centrioles. Centrioles also produce the aster microtubules that are very important for cell division.
29. What are mitochondria? What is the basic morphology of these organelles and in which cells can they be found?
Mitochondria are the organelles in which the most important part of cellular respiration occurs: ATP production.
Mitochondria are organelles enclosed by two lipid membranes. The inner membrane invaginates to the interior of the organelle, forming the cristae that enclose the internal space known as the mitochondrial matrix, in which mitochondrial DNA (mtDNA), mitochondrial RNA (mt RNA), mitochondrial ribosomes and respiratory enzymes can be found. Mitochondria are numerous in eukaryotic cells and they are even more abundant in cells that use more energy, such as muscle cells. Because they have their own DNA, RNA and ribosomes, mitochondria can self-replicate.
30. Why can mitochondria be considered the "power plants" of aerobic cells?
Mitochondria are the “power plants” of aerobic cells because, within them, the final stages of the cellular respiration process occur. Cellular respiration is the process of using an organic molecule (mainly glucose) and oxygen to produce carbon dioxide and energy. The energy is stored in the form of ATP (adenosine triphosphate) molecules and is later used in other cellular metabolic reactions. In mitochondria, the two last steps of cellular respiration take place: the Krebs cycle and the respiratory chain.
31. What is the endosymbiotic hypothesis regarding the origin of mitochondria? What molecular facts support this hypothesis? To which other cellular organelles can the hypothesis also be applied?
It is presumed that mitochondria were primitive aerobic prokaryotes that were engaged in mutualism with primitive anaerobic eukaryotes, receiving protection from these organisms and providing them with energy in return. This hypothesis is called the endosymbiotic hypothesis of the origin of mitochondria.
This hypothesis is strengthened by some molecular evidence, such as the fact that mitochondria have their own independent DNA and protein synthesis machinery, as well as their own RNA and ribosomes, and that they can self-replicate.
The endosymbiotic theory can also be applied to chloroplasts. It is assumed that these organelles were primitive photosynthetic prokaryotes because they have their own DNA, RNA and ribosomes, and can also self-replicate.
32. What are the main components of the cytoskeleton?
The cytoskeleton is a network of very small tubules and filaments distributed throughout the cytoplasm of eukaryotic cells. It is made of microtubules, microfilaments and intermediate filaments.
Microtubules are formed by molecules of a protein called tubulin. Microfilaments are made of actin, the same protein that is involved in the contraction of muscle cells. Intermediate filaments are also made of protein.
33. What are the functions of the cytoskeleton?
As the name indicates, the cytoskeleton is responsible for maintaining of the normal shape of the cell. It also facilitates the transport of substances across the cell and the movement of cellular organelles. For example, the interaction between actin-containing filaments and the protein myosin creates pseudopods. In the cells of the phagocytic defense system, such as macrophages, the cytoskeleton is responsible for the plasma membrane projections that engulf the external material to be interiorized and attacked by the cell.
34. What are chloroplasts? What is the main function of chloroplasts?
Chloroplasts are organelles present in the cytoplasm of plant and algae cells. Like mitochondria, chloroplasts have two boundary membranes and many internal membranous sacs. Within the organelle, DNA, RNA ribosomes and also the pigment chlorophyll are present. The latter is responsible for the absorption of the light photic energy used in photosynthesis.
The main function of chloroplasts is photosynthesis: the production of highly energetic organic molecules (glucose) from carbon dioxide, water and light.
35. What is the molecule responsible for the absorption of light energy during photosynthesis? Where is that molecule located in photosynthetic cells?
Chlorophyll molecules are responsible for the absorption of light energy during photosynthesis. These molecules are found in the internal membranes of chloroplasts.
36. What colors (of the electromagnetic spectrum) are absorbed by plants? What would happen to photosynthesis if the green light waves that reach a plant were blocked?
Chlorophyll absorbs all other colors of the electromagnetic spectrum, but it does not absorb green. Green is reflected and such reflection is the reason for that characteristic color of plants. If the green light that reaches a plant was blocked and exposure of the plant to other colors was maintained, there would be no harm to the photosynthesis process. This appears to be a paradox: green light is not important for photosynthesis.
There is a difference between the optimum color frequency for the two main types of chlorophyll, chlorophyll A and the chlorophyll B. Chlorophyll A has an absorption peak at a wavelength of approximately 420 nm (indigo) and chlorophyll B has its major absorption at a wavelength of 450 nm (blue).
37. What path is followed by the energy absorbed by plants to be used in photosynthesis?
The energy source of photosynthesis is the sun, the unique and central star of our solar system. In photosynthesis, solar energy is transformed into chemical energy, the energy of the chemical bonds of the produced glucose molecules (and of the molecular oxygen released). The energy of glucose is then stored as starch (a glucose polymer) or it is used in the cellular respiration process and transferred to ATP molecules. ATP is consumed during metabolic processes that require energy (for example, in active transport across membranes).
Plant Cell Wall and Vacuoles
38. What substance are plant cell walls made of? Which monomer is this substance made of?
Plant cell walls are made of cellulose. Cellulose is a polymer whose monomer is glucose. There are other polymers of glucose, such as glycogen and starch.
39. What is the function of plant cell walls?
Plant cell walls have structural and protective functions. They play an important role in limiting cell size, and stopping cells from bursting, when they absorb a lot of water.
40. What are plant cell vacuoles? What are their functions? What is the covering membrane of vacuoles called?
Plant cell vacuoles are cell structures enclosed by membranes within which there is an aqueous solution made of various substances such as carbohydrates and proteins. In young plant cells, many small vacuoles can be seen within adult cells, the majority of the internal area of the cell is occupied by a central vacuole.
The main function of vacuoles is the osmotic balance of the intracellular space. They act as “an external space” inside the cell. Vacuoles absorb or release water in response to cellular metabolic necessities by increasing or lowering the concentration of osmotic particles dissolved in the cytosol. Vacuoles also serve as a place for the storage of some substances.
The membrane that encloses vacuoles is called the tonoplast, named after the osmotic function of the structure.
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This research was largely supported by the Lawrence Berkeley National Laboratory (LBNL) Genomes to Watershed Scientific Focus Area funded by the US Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research (OBER) under contract no. DE-AC02-05CH11231. Additional support was provided by LBNL EFRC award no. DE-AC02-05CH11231, NASA NESSF grant no. 12-PLANET12R-0025 and NSF DEB grant no. 1406956, DOE OBER grant no. DOE-SC10010566, Office of Naval Research grants nos. N00014-07-1-0287, N00014-10-1-0233 and N00014-11-1-0918, and by the Thomas C. and Joan M. Merigan Endowment at Stanford University. In addition, funding was provided by the Ministry of Economy, Trade and Industry of Japan. The authors thank J. Eisen for comments, S. Venn-Watson, K. Carlin and E. Jensen (US Navy Marine Mammal Program) for dolphin samples, K.W. Seitz for sequence submission assistance, and the DOE Joint Genome Institute for generating the metagenome sequence via the Community Science Program.
Reproduction in the Protozoa may be asexual, as in the amebas and flagellates that infect humans, or both asexual and sexual, as in the Apicomplexa of medical importance. The most common type of asexual multiplication is binary fission, in which the organelles are duplicated and the protozoan then divides into two complete organisms. Division is longitudinal in the flagellates and transverse in the ciliates amebas have no apparent anterior-posterior axis. Endodyogeny is a form of asexual division seen in Toxoplasma and some related organisms. Two daughter cells form within the parent cell, which then ruptures, releasing the smaller progeny which grow to full size before repeating the process. In schizogony, a common form of asexual division in the Apicomplexa, the nucleus divides a number of times, and then the cytoplasm divides into smaller uninucleate merozoites. In Plasmodium, Toxoplasma, and other apicomplexans, the sexual cycle involves the production of gametes (gamogony), fertilization to form the zygote, encystation of the zygote to form an oocyst, and the formation of infective sporozoites (sporogony) within the oocyst.
Some protozoa have complex life cycles requiring two different host species others require only a single host to complete the life cycle. A single infective protozoan entering a susceptible host has the potential to produce an immense population. However, reproduction is limited by events such as death of the host or by the host's defense mechanisms, which may either eliminate the parasite or balance parasite reproduction to yield a chronic infection. For example, malaria can result when only a few sporozoites of Plasmodium falciparum—perhaps ten or fewer in rare instances𠅊re introduced by a feeding Anopheles mosquito into a person with no immunity. Repeated cycles of schizogony in the bloodstream can result in the infection of 10 percent or more of the erythrocytesout 400 million parasites per milliliter of blood.
Cells dissociated from various tissues of vertebrate embryos preferentially reassociate with cells from the same tissue when they are mixed together. This tissue-specific recognition process in vertebrates is mediated mainly by a family of Ca 2+ -dependent cell-cell adhesion proteins called cadherins, which hold cells together by a homophilic interaction between these transmembrane proteins on adjacent cells. For this interaction to be effective, the cytoplasmic part of the cadherins must be linked to the cytoskeleton by cytoplasmic anchor proteins called catenins.
Two other families of transmembrane adhesion proteins have major roles in cell-cell adhesion. Selectins function in transient Ca 2+ -dependent cell-cell adhesions in the bloodstream by binding to specific oligosaccharides on the surface of another cell. Members of the immunoglobulin superfamily, including N-CAM, mediate Ca 2+ -independent cell-cell adhesion processes that are especially important during neural development.
Even a single cell type uses multiple molecular mechanisms in adhering to other cells (and to the extracellular matrix). Thus, the specificity of cell-cell (and cell-matrix) adhesion seen in embryonic development must result from the integration of several different adhesion systems, of which some are associated with specialized cell junctions, while others are not.