Hands-on learning is known to be more effective for teaching science to students, even the most basic molecular and synthetic biology experiments require equipment far beyond an average classroom’s budget and bacteria and other substances that can be difficult to manage outside of a controlled laboratory setting.
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Now, a collaboration among Northwestern University, the Massachusetts Institute of Technology and the Wyss Institute at Harvard University is aiming to solve this problem with BioBits, new educational biology kits that use freeze-dried cell-free (FD-CF) reactions to enable students to perform a range of simple, hands-on biological experiments. The BioBits kits introduce molecular and synthetic biology concepts without the need for specialized lab equipment, at a fraction of the cost of current standard experimental designs.
“We wanted to create low-cost, educational kits that can be used in the classroom for less than $100,” said Michael Jewett, the Charles Deering McCormick Professor of Teaching Excellence and associate professor of chemical and biological engineering in Northwestern’s McCormick School of Engineering.
The kits are described in two papers (BioBits Bright and BioBits Explorer) published Aug. in the journal Science Advances. Jewett, who also is the co-director of Northwestern’s Center for Synthetic Biology, and Jim Collins, the Termeer Professor of Medical Engineering & Science at MIT, served as the paper’s co-corresponding authors.
“The main motivation in developing these kits was to give students fun activities that allow them to actually see, smell and touch the outcomes of the biological reactions they’re doing at the molecular level,” said Ally Huang, a co-first author on both papers and a graduate student in Collins’ lab. “My hope is that they will inspire more kids to consider a career in STEM and, more generally, give all students a basic understanding of how biology works because they may one day have to make personal or policy decisions based on modern science.”
Synthetic and molecular biology frequently make use of the cellular machinery found in E. coli bacteria to produce a desired protein. But this system requires that the bacteria be kept alive and contained for an extended period of time and involves several complicated preparation and processing steps. The FD-CF reactions pioneered in Collins’ lab for molecular diagnosticscombined with innovations in cell-free synthetic biology from Jewett’s lab bypass this issue by removing bacteria from the equation altogether.
“You can think of it like opening the hood of a car and taking the engine out,” Jewett said. “We’ve taken the ‘engine’ that drives protein production out of a bacterial cell and given it the fuel it needs, including ribosomes and amino acids, to create proteins from DNA outside of the bacteria itself.”
This collection of molecular machinery is then freeze-dried into pellets so that it becomes shelf-stable at room temperature. To initiate the transcription of DNA into RNA and the translation of that RNA into a protein, a student just needs to add the desired DNA and water to the freeze-dried pellets.
The researchers designed a range of molecular experiments that can be performed using this system, and coupled each of them to a signal that the students can easily detect with their senses of sight, smell or touch. The first, called BioBits Bright, contains six different freeze-dried DNA templates that each encode a protein that fluoresces a different color when illuminated with blue light.
“Challenging the students to build their own in vitro synthetic programs allows educators to start to talk about how synthetic biologists might control biology to make important products, such as medicines or chemicals,” said Jessica Stark, an NSF Graduate Fellow and graduate student in Jewett’s lab who is co-first author on both papers.
Students used the BioBits kits to perform experiments with the same success as trained synthetic biology researchers.
An expansion of the BioBits Bright kit, called BioBits Explorer, includes experiments that engage the senses of smell and touch and allow students to probe their environment using designer synthetic biosensors. One experiment, for example, uses a sensor that glows fluorescent when in the presence of banana or a kiwi DNA. Another experiment creates a compound that smells like bananas. The third experiment results in a squishy hydrogel, which students can touch and manipulate.
Researchers tested their BioBits kits in the Chicago Public School system and noticed that students and teachers could perform the experiments with the same success as trained synthetic biologists. Jewett said, “We have been so lucky to partner and work closely with the Office of Community Education Partnerships at Northwestern, who have a deep network of collaborators and know-how to connect to students in the Chicago area.” The team next plans to refine the kits’ design and create an open-source online database where teachers and students can share their results and ideas to modify the kits to explore different biological questions.
“Synthetic biology is going to be one of the defining technologies of the century, yet it has been challenging to teach the fundamental concepts of the field in K-12 classrooms given that such efforts often require expensive, complicated equipment,” Collins said. “We show that it is possible to use freeze-dried, cell-free extracts along with freeze-dried synthetic biology components to conduct innovative educational experiments in classrooms and other low-resource settings. The BioBits kits enable us to expose young kids, older kids, and even adults to the wonders of synthetic biology. “As a result,” Jewett added, “the Biobits kits are poised to transform science education and society.”
Last Updated on May 5, by Muhamed Elmesery
Molecular biology of the cell involves different macromolecules or biomolecules like proteins, carbohydrates, lipids, DNA and RNA (nucleic acids) and amino acids. Molecular biology studies their chemical and physical structures, compositions, modification, mechanisms, interactions, and functions which are essential and vital to life processes.
In this article, you will learn more about what is molecular biology, its techniques, how does it provide evidence for evolution, what is molecular biology central dogma? and a list of more than 35 molecular biology virtual lab experiments introduced by PraxiLabs.
Table of Contents
In simple words, molecular biology definition is the branch of science that is interested in studying various biological activities at the molecular level (between or in the cells).
To know what is molecular biology? Let’s take an overview at the science of molecular biology.
The origin of molecular biology began in the s with the convergence of various, previously distinct branches of biological and physical science, such as microbiology, biochemistry, genetics, physics, and more. Because of the desire to understand life at its most fundamental level, several scientists in chemistry and physics also took an interest in what would become molecular biology. In its modern sense, molecular biology attempts to explain the phenomena of life starting from the macromolecular properties that generate them.
Two categories of macromolecules in particular are the focus of the molecular biologists:
One definition of the scope of molecular biology therefore, is to characterize the structure, function and relationships between these two types of macromolecules. This relatively limited definition will suffice to allow us to establish a date for the so-called “molecular revolution”, or at least to establish a chronology of its most fundamental developments.
In , the term molecular biology was used by the physicist William Astbury. In , Francis Crick, James Watson, Rosalind Franklin, and colleagues, working at the Medical Research Council unit, Cavendish laboratory, Cambridge (now the MRC Laboratory of Molecular Biology), made a double helix model of DNA which changed the entire research scenario. They proposed the DNA structure based on previous research done by Rosalind Franklin and Maurice Wilkins. This research then led to finding DNA material in other microorganisms, plants and animals.
The central dogma of molecular biology is a theory that explains that the flow of genetic information (from DNA to RNA to protein) occurs only in one direction to make a functional product. The central dogma of molecular cell biology says that our DNA contains the needed information to make all of our proteins, and the role of RNA is a messenger that carries this information to the ribosomes. The role of these ribosomes is that they act as cell factories where the process of information translation from a code into the functional (final) product happens.
The process of gene expression has 2 stages that are called transcription and translation. In the transcription stage, the information which is found in the DNA of the cell is converted into messages that are portable and small. However in translation, the messages travel or translate from where the DNA is in the cell nucleus to the ribosomes to make specific proteins.
The central dogma of molecular biology states that the pattern of information that occurs in our cells is:
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Example:
One gene might code for eye color. The gene is used by cells to make proteins that create green pigment in our eyes
Molecular biology techniques are the methods used in molecular biology and other related branches like genetics, biochemistry and biophysics which generally involve processes like modification, interaction, manipulation and analysis of DNA , protein, RNA and lipid.
Let’s put a spotlight on some of the most common molecular biology techniques:
Polymerase chain reaction or PCR is one of the most important methods in molecular biology. It is basically a test tube system for DNA replication that is used to copy DNA and allows a target DNA sequence (single) to be amplified into millions of DNA molecules folds in just a few hours. PCR can also be used to introduce and detect mutations within the DNA or the sites of special restriction enzymes. PCR is also used to detect whether a certain DNA fragment exists in a cDNA library.
In addition, PCR is used widely in the medical and biological fields for a variety of applications such as DNA cloning for sequencing, functional gene analysis, and the diagnosis and detection of hereditary and infectious diseases.
There are many different types of PCR like:
Gel electrophoresis is an important molecular biology method used to separate mixtures of DNA, RNA, and proteins depending on their molecular size. In this technique, the molecules to be separated are run by an electric field through agarose gel that contains small pores and that allows you to differentiate between DNA fragments of different lengths.
There are many applications of gel electrophoresis like:
DNA cloning is a molecular biology technique that is used to make several identical copies of a piece of DNA, such as a gene or other DNA pieces. DNA cloning is done by inserting a target gene into a circular piece of DNA which is called “plasmid”. Then, through the transformation process, the plasmid is introduced into bacteria (selected by using antibiotics). These bacteria are used to make more plasmid DNA or, induced to express the gene and make protein.
The cloned DNA can be used to:
Cell culture is one of the most important molecular cell biology techniques as it provides a platform to investigate the biology, physiology (e.g., aging), biochemistry, and cells and diseased cells metabolism. It is also used to study mutagenesis, carcinogenesis, the effects of drugs and toxic compounds on the cells, and the route of infection and interaction between wild-type cells and pathogenic agents (e.g., fungi, bacteria and viruses).
Cell culture is the process by which human, animal, or plant cells are removed and grown in an artificial environment under controlled condition. For example, cultured animal cells are used in the production of viruses, and these viruses are used to produce vaccines. For example, vaccines for diseases like rabies, chicken pox, polio, measles and hepatitis B are produced using culture of animal cell.
We can define DNA extraction as the technique that is used to isolate DNA by breaking the cell and nuclear membrane with the help of some chemical substances or enzymes or physical disruptions. DNA extraction has been the target of a lot of research, as it has many applications like genetic modification of plants, detecting bacteria, and viruses in the environment, altering animals, medical diagnosis, paternity tests, identity verification, pharmaceutical products, and hormone production.
The extraction of DNA is critical to molecular cell biology and biotechnology. It is considered the first step of different applications, varying from routine diagnostic and therapeutic decision-making to fundamental research. The importance of DNA extraction and purification is that they are vital and essential for defining the unique characteristics of DNA, such as its shape, size, and function.
Investigation of the DNA sequence and structure that are related to diseases helped in finding out the molecular basis and cure for various diseases. DNA extraction also allowed the scientists to produce many vaccines, enzymes, and hormones. As well as it was also very beneficial and important in the forensic/medico legal entities.
To study DNA, it must be extracted out of the cell. Hence, DNA extraction technique is widely used in research labs.
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CRISPR (clustered regularly interspaced short palindromic repeats) is a technology that researchers use to selectively modify the DNA of living organisms.
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The CRISPR renaissance was catalyzed by the discovery that RNA-guided prokaryotic CRISPR-associated (Cas) proteins can create targeted double-strand breaks in mammalian genomes. This finding led to the development of CRISPR systems that harness natural DNA repair mechanisms to repair deficient genes more easily and precisely than ever before.
CRISPR has been used to knock out harmful mutant genes and to fix errors in coding sequences to rescue disease phenotypes in preclinical studies and in several clinical trials.
However, most genetic disorders result from combinations of mutations, deletions, and duplications in the coding and non-coding regions of the genome and therefore require sophisticated genome engineering strategies beyond a simple gene knockout.
To overcome this limitation, the toolbox of natural and engineered CRISPR–Cas systems has been dramatically expanded to include diverse tools that function in human cells for precise genome editing and epigenome engineering. The application of CRISPR technology to edit the non-coding genome, modulate gene regulation, make precise genetic changes ,and target infectious diseases has the potential to lead to curative therapies for many previously untreatable diseases.
A study proves that the ease with which CRISPR can create targeted DSBs in the human genome , which enabled quick adoption as a broad tool to overcome genetic disorders. As a first step, CRISPR was used to perform targeted gene knockouts, as Cas9 can be targeted anywhere on the coding sequence to induce a frameshift mutation to silence a deleterious protein.
However, most diseases are complex and cannot be cured by this simple coding sequence-targeting strategy. The use of CRISPR to target diseases with complex drivers has been catalyzed by developing more nuanced strategies that target the non-coding genome and indirectly modify gene expression (for example, by exon skipping or intron corrections).
Beyond these approaches, the rapid discovery of natural CRISPR molecules with beneficial properties and further engineering of these proteins to create molecules that alter transcription, change the epigenome, make precise mutations or enable writing directly onto the genome have dramatically increased the range of indications that can potentially be treated using CRISPR–Cas systems. However, further advances are needed to fully leverage these proteins.
The use of CRISPR tools to target more nuanced disease drivers requires a better understanding of how non-coding DNA and epigenetic states affect disease pathology.
Point mutations in coding sequences are much easier to link to a disease phenotype than mutations in non-coding sequences owing to a deep understanding of how a genetic change results in an amino acid change by looking at sequencing information. Using the right CRISPR tool that can link sequence, epigenome, transcriptome and phenotype information to the root cause of a pathology that is not driven by simple polymorphisms, it will be helpful in defining new cures.
However, the rapid advances in CRISPR tools, multi-omic methods and delivery mechanisms indicate that genome engineering techniques will soon be developed for a multitude of diseases, potentially resulting in curative therapies for many underserved patient populations.
Study: Advances in CRISPR therapeutics | Nature
The basics of molecular biology mainly focus on understanding the interactions between the various components of a cell, including the interactions between DNA (deoxyribonucleic acid), RNA (Ribonucleic acid) and protein biosynthesis as well as learning how these interactions occur and are regulated.
Human DNA is 98% identical to that of a chimpanzee, while it is 40-50% identical to that of a cabbage.
If you could write 60 words per minute, and you continued to work 8 hours a day, it would take 50 years to write the human genome.
The field of molecular biology looks at macromolecules found in living things and their chemical and physical structures, compositions, modifications, mechanisms, interactions, and functions which are essential and vital to life processes.
DNA extraction, DNA replication, gene expression, protein synthesis, DNA sequencing,the central dogma, transcription, cloning, and more.
Molecular biology techniques are the methods used in molecular biology and other related branches which generally involve processes like modification, interaction, manipulation and analysis of DNA , proteins, RNA and lipids.
Here are some of the most common molecular biology techniques:
The central dogma of molecular biology is a theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein.
Molecular biology’s classical period began in , with James Watson and Francis Crick’s discovery of the double helical structure of DNA (Watson and Crick a,b). Watson and Crick’s scientific relationship unified the various disciplinary approaches discussed above:
This series was established to create comprehensive treatises on specific topics in developmental biology. Such volumes serve a useful role in developmental biology, which is a very diverse field that receives contributions from a wide variety of disciplines. This series is a meeting ground for the various practitioners of this science, facilitating an integration of heterogeneous information on specific topics. Each volume comprises chapters selected to provide the conceptual basis for a comprehensive understanding of its topic as well as an analysis of the key experiments upon which that understanding is based.
The specialist in any aspect of developmental biology should understand the experimental background of the specialty and be able to place that body of information in context, in order to ascertain where additional research would be fruitful. The creative process then generates new experiments. This series is intended to be a vital link in that ongoing process of learning and discovery.
The science of molecular biology provides data that supports the evolution theory. In particular, the DNA universality and the genetic code near universality for proteins show that all the living organisms once shared a common ancestor. DNA also provides clues and data about how evolution may have happened. The process of gene duplications allows one copy to undergo mutational events without harming an organism, as one copy continues to produce functional protein.
DNA sequences have also shed light on some of mechanism of Molecular biology and evolution . In general, the similarity of DNA sequence between groups of organisms shows their relatedness.
Nature Structural & Molecular Biology is a monthly peer-reviewed scientific journal publishing research articles, reviews, news, and commentaries in structural and molecular biology, with an emphasis on papers that show “functional and mechanistic”understanding of how molecular components in a biological process work together”.
It is published by the Nature Portfolio and was established in under the title Nature Structural Biology. Later, it obtained its current title in January . Like other Nature journals, there is no external editorial board, with editorial decisions being made by an in-house team, although peer reviewing by external expert referees forms a part of the review process.
According to the Journal Citation Reports, the journal had a impact factor of 15.369, ranking it the 13th out of 298 journals in the category “Biochemistry & Molecular Biology”, the 1st out of 72 journals in the category “Biophysics”, and the 16th out of 195 journals in the category “Cell Biology”.
So, if you are interested in Molecular biology news and articles, you can follow the Nature Structural & Molecular Biology journal.
Source
PraxiLabs provides a vast and exceptionally diverse collection of important molecular biology experiments with awesome features to improve students’ learning experience and outcomes.
Let’s take a look at some of PraxiLabs molecular biology virtual labs simulations!
The DNA extraction virtual lab from PraxiLabs lets students practice basic laboratory techniques and understand the protocol and principle involved in DNA extraction well. Students also will identify the role of reagents, techniques and equipment in the extraction of DNA. They will also know more about the importance and applications of DNA extraction.
After conducting the conventional PCR virtual experiment, students can demonstrate proficiency with the principle and protocol involved in PCR technique. They conclude downstream applications of conventional PCR.
In agarose gel electrophoresis simulation, students will learn how to identify and separate DNA or RNA molecules by size, the process of separation achieved by placing the molecules in a gel made up of small pores and setting an electric field across the gel. They will learn how to prepare an agarose gel properly, understand and visualize the precautions required during sample application in the gel. Students also will identify the role of reagents, techniques and equipment in the agarose gel electrophoresis experiments.
In DNA sequencing virtual lab, students will understand and learn:
In cDNA synthesis virtual lab, students will learn how to synthesize cDNA from RNA templates using the enzyme of reverse transcriptase.
By the end of the experiment, students will be able to understand the cDNA Synthesis protocol well which is one of the important Concepts in Molecular Biology, practice the basic laboratory techniques proficiency, and identify the role of specific equipment and reagents that are used in cDNA Synthesis.
In the plating out technique experiment (streak plate method) virtual lab, students will learn how to isolate bacteria from a mixed population into a pure culture of the organisms by streak plate method. They also will become proficient at doing streak plate method accurately and consistently, produce isolated organism colonies on an agar plate, and learn organism identification by performing biochemical tests to identify bacteria (organism) that are only valid when performed on pure cultures.
By the end of DNA fingerprinting using gel electrophoresis simulation, students will be able to:
In the oxidase test virtual lab, students will learn how to detect if an organism possesses the cytochrome oxidase enzyme. By conducting this test they will be able to differentiate between oxidase positive species like Moraxella, Neisseria, Campylobacter, Pasteurella, and pseudomonads species.
In antibiotic sensitivity test disc diffusion method simulation, the students will learn how to determine the susceptibility of a microbial species against different antibiotic agents, to utilize specific monitoring techniques to evaluate the susceptibility of a microbe to different antibiotics species, and to detect the range of antibiotic activity.
By the end of Real- Time PCR simulation, students will be able to:
In DNA microarray simulation, students will learn how to:
Learn how to practice the steps of cell fixation and permeabilization, and understand the concept of cell cycle analysis using propidium iodide in the flow cytometry cell cycle virtual lab.
By the end of XTT viability assay, students will be able to:
By the end of the experiment, students will be able to:
Be proficient at performing Haemagglutination tests procedure consistently and accurately, and learn the essential concepts of hematological tests.
By the end of the experiment, students will be able to :
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