Specimen

​​​​​​​​​​​​​​Specimen
n., plural: ​​​​​​​​​​​​​​specimens
[ˈspɛsɪmɪn]
Definition: An individual biological sample or organism used for scientific examination and study

A specimen is a meticulously selected representative of a group that undergoes rigorous research studies to derive some conclusions for the group; about its nature, activity, constitution, behavior, etc. In particular, a biological specimen refers to a living or non-living organism or any of its body parts that can serve as a point of reference when speaking about the entire group.

When embarking on scientific explorations within research laboratories or on fields, the concept of a “specimen” takes center stage. Imagine it as the ‘key protagonist’ in a captivating story of discovery. In such a narrative, a specimen is not just an ordinary entity; it’s a carefully chosen representative from the natural world that carries a wealth of insights and revelations within it.

In the world of biology, a specimen serves as a living or preserved representative which is meticulously selected to stand for an entire group, species, or phenomenon. Whether it’s a living organism, a tissue specimen, a fragment of ancient bone, or even a microscopic cell, each specimen is an integral focal point of research activities and exploration.

Researchers subject these specimens to meticulous analysis as they employ a set of techniques to decode their genetic makeup, unravel their chemical behaviors, or comprehend their structural intricacies or any other analysis depending on the overall goal of the work.

So, let’s dive into the details of this topic and read how specimens are constituted, selected, and studied. By the end, we’ll come to know how researchers delve deep into the specimen’s characteristics by studying its unique traits, behaviors, and genetic blueprints, thereby gathering profound insights into its larger physical, chemical, biological, ecological, evolutionary, or medical narratives.

Specimen Definition

In Biology, the definition of the specimen is as follows “a tangible piece of the natural world that scientists carefully select to represent a larger group of living organisms”. A biological specimen serves as a prime example that researchers study intensely to reveal the intricacies, constitution, nature, or behavior of a particular group of living organisms.

Some important basis on which scientists and researchers select an ideal specimen for studies are:

• It’s a representative of a larger group.
• It bears characteristics that other members of the group have.
• It is meticulously chosen for its characteristics or traits.
• Example: Flowering plants might serve as good specimens to delve into the intricacies of their growth patterns, reproductive processes, or responses to environmental changes.

In the case of living organisms, a specimen could be an individual typical animal, plant, or microorganism. This chosen individual becomes a window into understanding the broader population or species it belongs to.

NOTE: It is important to note that specimens aren’t just restricted to living beings. Even preserved samples like fossils, tissues, or cells that are no more living, but rather dead (non-living) can be specimens for biology researchers. Such specimens serve as time capsules offering snapshots of past life forms or cellular structures which aid in reconstructing evolutionary histories or unlocking medical mysteries. So, for biology students, a ‘specimen’ constitutes both living and non-living (dead) entities representative of a larger group.

• Specimen Etymology

The noun specimen is a 17th-century word, which has a meaning of a model or a pattern. It has been derived from the Latin word “spectere” meaning ‘to look’. This word is also used to describe “a kind of sample” like a specimen page or a specimen signature. A specimen signature is a sample signature usually submitted to banks as a reference for all documents and debit/credit purposes.

Specimen in Other Fields of Science

The concept of a specimen is relevant and utilized across various fields of science and not just Biology. In essence, across diverse scientific fields, a specimen serves as a tangible and representative entity that scientists scrutinize to glean insights, answer questions, and advance knowledge in their respective disciplines. Here’s how it applies in different disciplines apart from Biology:

1. Paleontology: In the study of ancient life, specimens often refer to fossils which are preserved remains of prehistoric plants, animals, or other organisms. These fossils provide crucial clues about Earth’s history, evolution, and the past environments in which these creatures lived.

   

2. Geology: Geological specimens could be rocks, minerals, or sediment samples extracted from different parts of the Earth’s crust. Geologists analyze these specimens to unravel Earth’s geological processes, history, and the composition of its layers.

   

3. Astronomy: In the context of space science, specimens could refer to extraterrestrial materials such as meteorites or lunar samples collected from the Moon. Studying these specimens helps scientists understand the origins of our solar system and the broader universe.

   

4. Chemistry: In chemistry, specimens might include samples of chemicals, compounds, or elements. These samples are analyzed to determine their properties, behavior, and interactions. This aids in the advancement of chemical knowledge and applications.
5. Medicine: In the medical field, specimens usually refer to samples taken from patients for diagnostic examination purposes. These could include blood, urine, tissue biopsies, or even swabs. Analyzing medical specimens helps diagnose diseases, monitor health, and develop treatments.

   

6. Archaeology: Archaeological specimens encompass artifacts, pottery, tools, bones, and other materials from past human civilizations. These specimens shed light on ancient cultures, technologies, and ways of life.
7. Physics: In physics, specimens could be samples of materials used in experiments like crystals, metals, or superconductors. These specimens are subjected to various tests to explore their physical properties and behaviors.

Watch this vid about ​​​​​​​​​​​​​​specimen collection in a medical setting:

What Are Examples Of Specimens?

Here’s a table illustrating examples of specimens in various scientific fields.

Data Source: Dr. Harpreet Narang of Biology Online

NOTE IT!

DNA Extraction and Amplification from Dead Biological Specimens

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DNA extraction from ancient biological specimens is a complex and delicate process that allows scientists to recover genetic material from preserved remains. This technique has been instrumental in discovering the genetic history of extinct species, tracing evolutionary relationships, and understanding past populations. The utilization of herbarium specimens and museum wet collection specimens for extraction of quality DNA also becomes possible in such a manner. (Ref-9, 10, 11)

Here’s an overview of the steps involved in DNA extraction from ancient, preserved, or herbarium specimens:

1. Sample Selection:

   

   The first step is selecting an appropriate sample. This could be bone, tooth, hair, or herbarium specimens that have been preserved over time often in environments like permafrost, caves, or arid conditions which slow down the degradation of DNA or lab settings as in herbarium sheets).

2. Surface Decontamination: The exterior of the specimen may have been exposed to different contaminants like human DNA from handling. To minimize this, researchers often sterilize the exterior of the specimen before extraction.
3. Powdering: In some cases, the specimen needs to be mechanically reduced to a powder form. This increases the surface area for DNA extraction and allows for more effective chemical treatment.
4. Chemical Treatment: The powdered sample is then subjected to various chemical treatments which can include “digestion with enzymes” that break down cellular material and the “use of detergents” (like SDS, CTAB, Nonidet P-40, Twin20, Triton X100, Sarkosyl) to lyse cell membranes and release DNA.

   

   • A shows the amphipathic nature of CTAB with a long hydrocarbon chain (also called the “hydrophobic tail”) and a positively charged tri-methyl-ammonium group (also called the “hydrophilic head”).
   • B shows the micelle formation by CTAB molecules in the aqueous solution where the polar heads (hydrophilic) are facing outside while the non-polar tails (hydrophobic) are facing inside.
   • C shows the structure of the biological plasma membrane which is made up of amphipathic lipid molecules with integral protein (black).
   • D shows how CTAB pulls off the plasma membrane lipids and aid in the formation of a “hybrid micelle”.

   Image Credit: Heikrujam, J. (2020) 

• DNA Extraction: Following the chemical treatment, DNA is extracted using methods such as “phenol-chloroform extraction” or “commercial DNA extraction kits”. These methods separate DNA from other cellular components and contaminants.
• DNA Purification: Extracted DNA may still contain impurities and inhibitors that can interfere with subsequent analyses. Purification steps including precipitation and column-based purification help remove these contaminants.

  

• Amplification: Ancient DNA is often degraded into short fragments. Polymerase chain reaction (PCR) is used to selectively amplify the target DNA regions. Specialized DNA polymerases like Taq polymerase with proofreading capabilities are used to reduce errors.

It’s important to note that DNA extraction from ancient specimens is challenging due to the degraded and often contaminated nature of the samples. Researchers must take rigorous precautions to prevent contamination and use specialized techniques to ensure the reliability of the results. When isolated properly, DNA extracted from ancient specimens can provide valuable insights into the genetic history and evolution of various species, including our own. ☺

Take the ​​​​​​​​​​​​​​Specimen – Biology Quiz!

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References

1. Hofman, L. F. (2001). Human saliva as a diagnostic specimen. The Journal of Nutrition, 131(5), 1621S-1625S.
2. Fakheran, O., Dehghannejad, M., & Khademi, A. (2020). Saliva as a diagnostic specimen for detection of SARS-CoV-2 in suspected patients: a scoping review. Infectious diseases of poverty, 9(04), 3-9.
3. Zhang, J., Wang, S., & Xue, Y. (2020). Fecal specimen diagnosis 2019 novel coronavirus–infected pneumonia. Journal of medical virology, 92(6), 680-682.
4. Rao, D. S., Muraleedharan, K., & Humphreys, C. J. (2010). TEM specimen preparation techniques. Microscopy: science, technology, applications and education, 2, 1232.
5. Jones, B. A., Calam, R. R., & Howanitz, P. J. (1997). Chemistry specimen acceptability. Archives of pathology & laboratory medicine, 121(1), 19.
6. Ibrahim, Y. S., Tuan Anuar, S., Azmi, A. A., Wan Mohd Khalik, W. M. A., Lehata, S., Hamzah, S. R., … & Lee, Y. Y. (2021). Detection of microplastics in human colectomy specimens. JGH open, 5(1), 116-121.
7. Rocha, L. A., Aleixo, A. L. E. X. A. N. D. R. E., Allen, G., Almeda, F., Baldwin, C. C., Barclay, M. V., … & Witt, C. C. (2014). Specimen collection: an essential tool. Science, 344(6186), 814-815.
8. Popescu, D., Zapciu, A., Amza, C., Baciu, F., & Marinescu, R. (2018). FDM process parameters influence over the mechanical properties of polymer specimens: A review. Polymer Testing, 69, 157-166.
9. Marinček, P., Wagner, N. D., & Tomasello, S. (2022). Ancient DNA extraction methods for herbarium specimens: When is it worth the effort? Applications in plant sciences, 10(3), e11477. https://doi.org/10.1002/aps3.11477
10. Straube, N., Lyra, M. L., Paijmans, J. L. A., Preick, M., Basler, N., Penner, J., Rödel, M. O., Westbury, M. V., Haddad, C. F. B., Barlow, A., & Hofreiter, M. (2021). Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Molecular ecology resources, 21(7), 2299–2315. https://doi.org/10.1111/1755-0998.13433
11. Záveská Drábková L. (2021). Herbarium Specimens: A Treasure for DNA Extraction, an Update. Methods in molecular biology (Clifton, N.J.), 2222, 69–88. https://doi.org/10.1007/978-1-0716-0997-2_4
12. Särkinen, T., Staats, M., Richardson, J. E., Cowan, R. S., & Bakker, F. T. (2012). How to open the treasure chest? Optimizing DNA extraction from herbarium specimens.
13. Kates, H. R., Doby, J. R., Siniscalchi, C. M., LaFrance, R., Soltis, D. E., Soltis, P. S., … & Folk, R. A. (2021). The effects of herbarium specimen characteristics on short-read NGS sequencing success in nearly 8000 specimens: Old, degraded samples have lower DNA yields but consistent sequencing success—frontiers in plant science, 12, 669064.
14. Heikrujam, J., Kishor, R., & Mazumder, P. B. (2020). The chemistry behind plant DNA isolation protocols. Biochem. Anal. Tools–Methods Bio-Molecules Stud, 8, 131-141.

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