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molecular biology , field of science concerned with studying the chemical structures and processes of biological phenomena that involve the basic units of life, molecules . The field of molecular biology is focused especially on nucleic acids (e.g., DNA and RNA ) and proteins — macromolecules that are essential to life processes—and how these molecules interact and behave within cells . Molecular biology emerged in the 1930s, having developed out of the related fields of biochemistry , genetics , and biophysics ; today it remains closely associated with those fields.

Various techniques have been developed for molecular biology, though researchers in the field may also employ methods and techniques native to genetics and other closely associated fields. In particular, molecular biology seeks to understand the three-dimensional structure of biological macromolecules through techniques such as X-ray diffraction and electron microscopy . The discipline particularly seeks to understand the molecular basis of genetic processes; molecular biologists map the location of genes on specific chromosomes , associate these genes with particular characters of an organism, and use genetic engineering (recombinant DNA technology) to isolate, sequence, and modify specific genes. These approaches can also include techniques such as polymerase chain reaction , western blotting, and microarray analysis.

In its early period during the 1940s, the field of molecular biology was concerned with elucidating the basic three-dimensional structure of proteins. Growing knowledge of the structure of proteins in the early 1950s enabled the structure of deoxyribonucleic acid (DNA)—the genetic blueprint found in all living things—to be described in 1953. Further research enabled scientists to gain an increasingly detailed knowledge not only of DNA and ribonucleic acid (RNA) but also of the chemical sequences within these substances that instruct the cells and viruses to make proteins.

Molecular biology remained a pure science with few practical applications until the 1970s, when certain types of enzymes were discovered that could cut and recombine segments of DNA in the chromosomes of certain bacteria . The resulting recombinant DNA technology became one of the most active branches of molecular biology because it allows the manipulation of the genetic sequences that determine the basic characters of organisms.

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Methods in molecular biology and genetics: looking to the future

Diego a. forero.

1 School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia

Vaibhav Chand

2 Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, USA

Associated Data

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In recent decades, advances in methods in molecular biology and genetics have revolutionized multiple areas of the life and health sciences. However, there remains a global need for the development of more refined and effective methods across these fields of research. In this current Collection, we aim to showcase articles presenting novel molecular biology and genetics techniques developed by scientists from around the world.

A brief overview of the development of methods of molecular biology and genetics

Since ancient times, humankind has recognized the influence of heredity, based on familial resemblance, selective breeding of livestock, and climate-adapted crops. Prior to Gregor Johann Mendel’s work in the nineteenth century, there was no clear scientific theory to explain heredity. Mendel’s work remained essentially theoretical until the discovery of DNA and confirmation of its role as the principal agent of heredity in organisms in the twentieth century [ 1 ]. In addition, the resolution of the DNA structure paved the way for the invention of the Polymerase Chain Reaction (PCR) (by Kary Mullis), nucleotide synthesis [ 2 ] and the Sanger sequencing method [ 3 ] which revolutionized the field of genetics and led to the development of several sub-disciplines, including cytogenetics, biotechnology, bioprocess technology, and molecular biology. Automation of Sanger sequencing led to the Human Genome Project in 1990 [ 1 ], soon followed by sequencing the complete genomes of numerous other species of flora and fauna [ 4 ].

In recent decades, advances in methods in molecular biology and genetics have revolutionized multiple areas of life and health sciences [ 2 ]. As a major example from health sciences, PCR-based methods have advanced our understanding of the aetiology of a myriad of acute and chronic diseases, in addition to allowing the diagnosis of multiple disorders [ 1 , 5 ]. As a recent global application of molecular methods, the PCR-based approaches have led to the processing of hundreds of millions of samples for the analysis of the SARS-CoV-2 virus [ 6 ]. In addition, molecular methods have been key for the creation of multiple companies, products and jobs [ 7 ].

The development of sequencing technologies and their iterative improvements have been instrumental in advancing the understanding of DNA and RNA, their identification, association with various proteins, their covalent modifications, the function of the genes they carry, and the function of the non-coding portion of DNA and RNA in normal and diseased cells, in pathogenic bacteria and viruses, and in plants [ 8 , 9 ]. By producing RNA-based vaccines, we were able to combat the recent SARS-CoV2 pandemic. This was made possible by sequencing and in vitro nucleotide synthesis technologies [ 10 ].

Gene editing technologies, such as restriction endonuclease digestion, transcription activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR-Cas) system, are an additional development in the field of molecular biology that has aided in the understanding of DNA and genes. There is optimism about the use of CRISPR-Cas9 technology in the treatment of a wide variety of diseases, such as cancer, blood-related diseases, hereditary blindness, cystic fibrosis, viral diseases, muscular dystrophy, and Huntington´s disease, due to its precision and its constant improvement, in comparison with other gene-editing technologies [ 15 ].

Need for novel methods in molecular biology and genetics

There is a global need for the development of novel methods for molecular biology and genetics. Particularly, in the area of human health, there is a need for further approaches that facilitate point-of-care molecular analysis (particularly miniaturized and portable platforms), for infectious and non-transmissible diseases [ 11 ], the development of more efficient methods for DNA sequencing [ 3 ], which facilitate cost-effective genome-wide analysis of patients, among others.

In addition, three key factors would also help push this field forward: additional research comparing the performance of different methods for molecular biology [ 12 ], the broader use of reporting standards (such as the Minimum Information for Publication of Quantitative Real-Time PCR Experiments -MIQE-, which describes details of experimental conditions) [ 13 ], and the increased participation of scientists from the Global South.

Although older techniques, such as x-ray crystallography, gene cloning, PCR, and sequencing, have been instrumental in the study of various aspects of genetics, these techniques have several limitations that result in gaps, missing links, and incomplete understanding of the genome. Advances in these techniques are needed to fill in these missing pieces of the puzzle to better comprehend genetics and accelerate the discovery of the causes of various genetically linkeddiseases. From a technological standpoint, the accuracy of sequencing and coverage across the genome remain major issues, especially for GC-rich regions and long homopolymer stretches of DNA. Furthermore, the short read lengths generated by the majority of current platforms severely restrict our ability to accurately characterize large repeat regions, numerous indels, and structural variation, rendering large portions of the genome opaque or inaccurate. Fragmentation of the genome for sequencing continues to be a major source of disruption in the continuity of the correct genomic sequence [ 14 , 15 ].

Recent advances in CRISPR technology provide hope for the medical treatment of cancer and other fatal diseases. Despite significant advances in this field, a number of technical obstacles remain, including off-target activity, insufficient indel or low homology-directed repair (HDR) efficiency, in vivo delivery of the Cas system components, and immune responses. This requires a substantial amount of technological advancement or the creation of new, superior methods to combat severe diseases with minimal side effects [ 14 , 16 ].

Additional considerations

As high-throughput, automated methods commonly produce very large amounts of data, deeper interaction between wet-lab and dry-lab researchers is required, to facilitate the design of efficient assays [ 17 ] and allow effective analysis and interpretation of results. Interdisciplinary collaborations, between biologists, engineers and professionals in the health sciences, might lead to newer and better methods of addressing current and future needs.

Further collaborations between scientists from academia and industry (in addition to researchers from government agencies) [ 18 ] would help to facilitate the development of novel methods, and aid in promoting their implementation around the world. For many countries, the main barrier to the broad use of molecular methods is the high cost of equipment and reagents [ 19 ]. Strategies aimed at lowering costs would be helpful for multiple institutions around the globe. In terms of intellectual property, fair licensing to institutions in the Global South as well as the implementation of Open Innovation and Open Science policies would be appropriate [ 20 ].

Overview of the current collection

In this current Collection, we are calling for articles showcasing novel methods from molecular biology and genetics, written by scientists from around the world. It is our goal to compile a set of articles that will help to address the challenges faced by the fields of molecular biology and genetics and broaden our understanding of genetic disorders and potential treatment strategies. We invite researchers working on such methods to consider submitting to our collection.

Acknowledgements

DAF has been previously supported by research grants from Minciencias and Areandina. VC has been previously supported by research grants from NIH and VA.

Author contributions

DAF and VC wrote an initial draft of the manuscript. All authors read and approved the final manuscript.

Data availability

Declarations.

DAF is a Senior Editorial Board Member of BMC Research Notes. VC is a Guest Editorial Board Member of BMC Research Notes.

DAF is a medical doctor, Ph.D. in Biomedical Sciences and Professor and Research Leader at the School of Health and Sport Sciences, Fundación Universitaria del Área Andina (Bogotá, Colombia). He has worked with multiple methods of molecular biology and genetics and is an author of more than 100 articles in international journals, has been peer reviewer for more than 115 international scientific journals, in addition to being part of editorial boards of several international journals. VC is a Research Assistant Professor in the Department of Biochemistry and Molecular Genetics at the University of Illinois at Chicago. His expertise in Biochemistry, Molecular Biology, Genetics, Oncology, and Cancer Biology is extensive. He is an invited reviewer for more than fourteen international peer review journals and is the author of fourteen articles with high impact.

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Contributor Information

Diego A. Forero, Email: oc.ude.anidnaera@14orerofd .

Vaibhav Chand, Email: ude.ciu@50dnahcv .

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Researchers decipher new molecular mechanisms related to biological tissue regeneration

by University of Barcelona

A new study published in The EMBO Journal opens new perspectives to better understand how the molecular mechanisms involved in regenerative medicine work.

The study focuses on tumor necrosis factor-α (TNF-α) and its receptors TNFR, molecules of key interest in biomedicine due to their involvement in multiple diseases such as obesity related to type 2 diabetes mellitus, inflammatory bowel disease and several types of cancer.

The study is led by Professor Florenci Serras, from the Faculty of Biology and the Institute of Biomedicine of the University of Barcelona (IBUB). The work also involves experts from the UB's Biodiversity Research Institute (IRBIO), the Center for Genomic Regulation (CRG) and the August Pi i Sunyer Biomedical Research Institute (IDIBAPS).

The work was also highlighted in the News & Views section of the journal in an article by Ditte S. Andersen and Julien Colombani.

The findings indicate that tumor necrosis factor-α (TNF-α)—a cellular activity modulating protein—has two TNFR receptors that can display completely opposite functions in response to biological tissue injury: Specifically, one receptor enhances cell survival and regeneration, while the other can promote cell death.

The study, carried out using the Drosophila melanogaster study model, could contribute to the design of TNFR receptor agonist and antagonist molecules that stimulate the regeneration of epithelial tissues in patients with severe burns, or affected by inflammatory bowel diseases and some cancers.

Drosophila: A model for studying human diseases

Communication between cells is a decisive process in the development and physiology of organisms. One of the pathways of cell communication is the secretion of molecules—e.g., tumor necrosis factor (TNF-α)—that have specific functions in biological cells, tissues and organs.

"In particular, the secreted tumor necrosis factor can recognize and bind to its receptor TNFR, which is located on the membrane of neighboring cells. As a result of the binding, the TNFR receptor is activated and regulates processes as diverse as cell proliferation, cell death and adaptive immunity," explains Serras, a member of the UB's Department of Genetics, Microbiology and Statistics.

In the mammalian genome, there are 19 TNF molecules and 29 TNFR receptors, which reveals the great complexity of their study in the case of the human species. However, some organisms such as the D. melanogaster fly have only one tumor necrosis factor (called Eiger, Egr) and only two TNFRs, which are the Grindelwald (Grnd) and Wengen (Wgn) receptors.

"Thanks to this simplicity, and adding the multiple genetic tools of Drosophila, we have been able to use this model organism to study the regulation and function of TNF-α/TNFR," says the researcher.

Receptors with opposing functions

Although TNF-α and TNFR receptors are linked to acute and chronic diseases, "it is still not well understood how these components regulate such opposing cellular processes as cell death or cell survival, and even cell proliferation ," Serras stresses.

This study, which will be included in the doctoral thesis to be defended by Ph.D. student José Esteban-Collado, provides evidence that supports the different and opposing functions of TNFR Grnd and Wgn. "On the one hand, the Grnd receptor promotes cell death (apoptosis) to eliminate damaged cells through a TRAF2-dTAK1-JNK signaling pathway in a TNF-α Egr-dependent manner," says Serras.

"In contrast, the Wgn receptor promotes cell survival and regeneration to keep tissues healthy and in good condition, via the TRAF1-Ask1-p38 signaling pathway and without the need for TNF-α Egr," he adds.

"That is, the first receptor needs the ligand to bind to the receptor, while the second can be activated without interacting with the ligand. Therefore, each TNFR promotes its signaling to achieve different functions," explains Serras. "Thus, the communication mechanisms of TNFRs must generate a balance between the activities of the different TNFRs, the molecular signals they set in motion and their dependence—or not—on the ligand (TNF-α)."

Damaged cells give off molecular signals in healthy cells

When a cell is dying or damaged, it communicates with healthy cells to replace the non-functional cell with a new one and initiate regeneration of the affected tissue. The research describes how dying cells release reactive oxygen species (ROS), which functional cells in their environment pick up to drive the regeneration process of the affected tissue.

"In a pathological situation or tissue damage , both receptors show different responses. First, the affected tissue produces TNF-α Egr, which binds to Grnd on the membrane. This is internalized and promotes suicide by cell death (apoptosis). At the same time, these cells produce ROS, which spread and reach healthy cells as an alarm signal indicating tissue deterioration," explains Serras.

"The ROS signal activates Wgn in healthy cells directly, without the need for Egr, and consequently triggers the signaling pathway that promotes tissue survival, protection and regeneration," notes Serras.

The results of the new study support the model in which ROS from damaged tissue can activate Wgn-dependent signaling in healthy surrounding cells to promote their regeneration.

Using an elegant binary system that allows manipulation of a gene in tissue-specific domains, the authors have also determined an essential role for TNFR Wgn—but not Grnd—in the activation of p38 kinase. "In healthy cells, this p38 will be responsible for setting in motion the entire genetic machinery for tissue repair," concludes Serras.

Ditte S Andersen et al, Wengen's hidden powers: ROS triggers a TNFR-dependent tissue regenerative pathway in Drosophila, The EMBO Journal (2024). DOI: 10.1038/s44318-024-00170-w

Journal information: EMBO Journal

Provided by University of Barcelona

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Friday Feature: Undergraduate Researcher Garrett Barksdale

This summer we're profiling recipients of  summer undergraduate research fellowships  to learn about their academic interests and glance into their daily lives as  undergraduate researchers .

Today we're speaking with MCB senior Garrett Barksdale, a member of the Wilfred van der Donk  lab and a 2024 recipient of the William T. and Lynn Jackson Summer Research Fellowship. 

Why did you decide to apply for a fellowship? I wanted to continue working on my research from the semester, and having the monetary support to stay on campus allowed me to do that. I had a fellowship last summer as well and it was a very positive experience.

How did you get involved in Dr. van der Donk’s lab? One of my TAs was an undergraduate researcher in the lab, and he helped get me a job as a lab technician. I did that for a semester, and then I got to join the lab as a researcher under one of the graduate students.

Tell us about your research interests and what you’re working on this summer. Our lab does natural product research with lanthipeptides, which are a type of ribosomally synthesized and post-translationally modified peptides, or RiPPs. The enzymes we study post-translationally modify these peptides. Right now, I’m testing enzyme variants and reaction rates with certain enzymes.

What does an average day look like for you? My days vary a lot, but I do have a little bit of a process. I’ll start by transforming e. Coli cells with the plasmids that will express the enzyme variants, and then I will express enzymes, purify them out and purify out the substrate. After all that prep work I can run reactions and see how the products are prepared and analyze them using liquid chromatography-mass spectrometry. It can take a couple of weeks to get to a point where I have useful data to analyze.

What do you hope to gain from this experience? I want to learn skills and techniques from the lab that I can transfer to future endeavors. I also just look forward to experiencing a lab environment, so I can figure out what I might be getting myself into in the future.

What are your career or academic goals? Eventually I’d like to go to grad school. In a perfect world, I think going into academia and having my own lab would be cool. For now, I’m thinking about jobs in industry.

Do you have any advice for other undergraduates who would like to get involved in research? Instead of waiting for specific times before or after the semester to email faculty members, reach out whenever you feel ready. The worst a professor can do is say no or just not respond. Also, be aware of nontraditional opportunities that could allow you to connect with a lab. It might seem like cold emailing is the only path, but you could be like me and start as a lab tech.

How do you like to spend your free time? After a long day in the lab, I love going back to my apartment and taking a nap. I also like playing video games and spending time with my five cats.

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