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What is a Protein? – Protein Data Bank/RCSB

April 19, 2019 at 3:17 pm / Molecular Nature, Video

Proteins are end products of the Central Dogma of biology. They are essential for cellular structure and function. Proteins have dizzyingly diverse structures. Since the invention of X-ray chrystallography by the Australian physicist William Lawrence Bragg structures of many complex molecules have been resolved including proteins. Solved structures of proteins are deposited in the Protein Data Bank (PDB), a free and curated structural data resource for thousands of biological molecules. These structures are stored in the form of Cartesian coordinates […]

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An Introduction to Zebrafish Brain

March 16, 2019 at 6:18 pm / Evolution, Molecular Nature, Video

What is consciousness? How do we learn complex coordinated movements like riding a bicycle and never forget afterwards? How does your brain know where your body ends and bicycle starts? The humble Zebrafish has all the clues to these questions and more. Systems simple enough to understand and complex enough to make generalizations always attracted scientists. The 80,000-neurons in the brain of the developing the zebrafish embryos provides one of those ideal systems to understand vertebrate brain evolution and function. […]

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A Virtual Tour of a Cell – XVIVO Scientific Animation (2018)

March 9, 2019 at 8:12 pm / Molecular Nature, Technical Notes, Video

The Cellscape is one of the many fascinating scientific visualizations created by XVIVO Scientific Animation Studio. The project was supported by Google Making and Science Team. The creators did a wonderful job in introducing us to the major parts of the cell visible to a viewer in the cytoplasm in a virtual environment. Conjuring the physico-chemical structures such as proteins and enzymes inside a cell is a rather difficult thing to do. The textbooks and diagrams, don’t do a justice […]

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An Annotated Animation of Zebrafish Embryo Development – Edwin Mutuma Murungi (2017)

March 3, 2019 at 7:37 pm / Evolution, Molecular Nature, Video

Evolutionarily speaking all of us are tetrapods and contain a fish inside! Take the retention of embryonic gill arches for example, still observed in quite a few people. Preaurucular pit is the scientific term for this ancestral structure. Its presence in Humans reflects the “evo-devo” aspect of our shared biological heritage with all vertebrates living on earth. Here, animated by Edwin Mutuma Murungi, the annotated animation of zebrafish embryo development produced by Norwegian University of Life Sciences – NMBU Learning […]

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The Axolotl: A Cut Above The Rest – Science Friday/Christian Baker (2016)

March 2, 2019 at 8:57 pm / Evolution, Molecular Nature, Natural history, Video, Wildlife Documentaries

Tissue regeneration is a fascinating biological subject. Many invertebrate organisms such as crabs, starfishes, sponges, jawless fish such as the lampreys and planarian flatworms can regenerate body parts. Among the vertebrates salamanders, especially the axolotl is a legendary study species for biologists. The axolotl is a highly endangered Mexican salamander with a fascinating ability to regenerate. Curiously, although both are amphibians salamanders can regenerate but frogs cannot. Comparison of such contrasting groups is particularly useful in understanding organ and tissue […]

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What Good are Introns Anyway? – Nature (2019)

February 6, 2019 at 2:56 pm / Molecular Nature, Video

Molecular Nature Introns are stretches of non-coding regions interspersed with the coding DNA in the genes of eukaryotic organisms. They are widespread, common and sometimes are ridiculously long stressing the economy of the cell. Burden of long introns is not limited to DNA replication which happens only once during cell division but continues to manifest itself at the transcription level where multiple rounds of RNA polymerase II activity consume energy proportional to the longevity of the cell. For instance, the […]

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Pygmy Seahorses as Masters of Camouflage – Deep Look – PBS/KQED (2015)

November 13, 2018 at 7:51 pm / Evolution, Molecular Nature, Natural history, Video

Environmental cues can have profound effects on the developmental trajectory of juveniles. When predatory dragonfly nymphs are present, tadpoles develop bigger tails with fast twitch muscles. Similarly the crustacean water fleas (Daphnia) develop helmet structures preventing fish to swallow them easily. Epigenetics is a relatively new branch of genetics but we have learned quite a lot in a few decades. The molecular mechanism of what evolutionary biologists described as phenotypic plasticity – biological ability to generate multiple phenotypes from a […]

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Gene Silencing by MicroRNAs – Katharina Petsche (2015)

November 21, 2017 at 8:25 am / Evolution, Molecular Nature, Video

Welcome to another post of Molecular Nature series highlighting a gene silencing mechanism known as RNA interference. The animation was produced by Katharina Petsche. The discovery was made by Craig Mello and Andrew Fire who shared 2006 Nobel Prize in Physiology and Medicine. Please keep in mind that this video is quite advanced in content and assumes the viewers know about basic molecular biological concepts such as the Central Dogma of Biology. RNA interference (RNAi) is a process used by […]

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Development of a Salamander Embryo – Yale University Department of Anatomy (1920s)

November 10, 2017 at 4:08 pm / Evolution, Molecular Nature, Technical Notes, Video

Everyone of us started life from one single cell formed by the fusion of an egg and a sperm. That single cell gave rise to every structure in our bodies. How did that happen? Salamanders are known to be able to regenerate limbs while frogs and lizards cannot. How and why? The time lapsed footage of salamander embryos developing from single fertilized eggs forms the basis of our morphological understanding of animal development. The footage recorded by Yale University researchers […]

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The Central Dogma of Biology – Kazufumi Watanabe (2008)

March 18, 2017 at 1:45 am / Evolution, Molecular Nature, Video

Riken Omics Center from Japan presents a well-crafted animation that summarizes one of the most important subjects of biology since 1958. The central dogma is our first systematic approach in understanding nature of the information flow and manufacture of structures within a living cell. The viewer must be warned that the structures in this animation are artistic representations and in reality they look quite different from space ships. For example RNA Polymerase II is one of the most well-studied enzymes […]

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Bacteria Evolution on a MEGA Petri Plate – Michael Baym – Harvard Medical School (2016)

September 10, 2016 at 10:36 pm / Evolution, Molecular Nature, Video

The Microbial Evolution and Growth Arena plate (MEGA-plate) experiment designed by Harvard Medical School researcher Michael Baym and his coworkers is an absolutely fascinating demonstration of evolution in action. They were able to visualize with a stunning didacticity (is that a word?) how bacteria evolves resistance to the antibiotic trimethoprim surprisingly fast for the Human time scale. The experiment is reminiscent of a highly simplified 2-D version of a long-term evolution experiment by Richard Lenski of the Michigan State University. […]

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Great Moments in Science with Dr Karl – Karl Kruszelnicki – Royal Institution (2015)

August 26, 2016 at 9:21 pm / Human Nature, Molecular Nature, Natural history, Video

Dr. Karl Kruszelnicki is an Australian science communicator with an amazing talent for concatenating subjects with a free-associative style. Just watch his whirlwind lecture full of interesting and eccentric facts and learn…

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Animations of Unseeable Biology – Drew Berry – TED Talk (2011)

June 3, 2016 at 7:00 am / Evolution, Molecular Nature, Video

Drew Berry introduces us to the fascinating world of molecules. Since the invention of X-ray crystallography our depth of understanding the molecular nature of things have skyrocketed. Year 2012 marked the centennial of the discovery of X-ray chrystallography by the Australian physicist William Lawrence Bragg who shared the Nobel Prize with his father in 1915. The technique was so powerful that since its discovery, it generated 28 Nobel Prizes including the discovery of DNA. the famous X-ray chrystallographical image #51 […]

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Decoding the Chemical Language of Nature – Jing-Ke Weng | TEDxBeaconStreet (2015)

May 6, 2016 at 9:17 pm / Evolution, Molecular Nature, Natural history

Chemical diversity in nature is bewildering. Repertoire of chemicals in plants is especially rich. A great majority (almost all) of the single-compound drugs have been discovered in plants: salicylic acid (Aspirin), artemisinin (anti-malarial), thebaine (analgesic derived from opium) are just a quick few to spell out. All these chemicals are products of specialized secondary metabolic pathways in plants. Chemical compounds forming specialized metabolites protect plants against various abiotic stresses and mediate an array of interspecies interactions, ranging from seduction of […]

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How Does the Purple Bacteria Photosynthesize? Beckman Institute-UIUC (2015)

March 28, 2016 at 11:03 am / Evolution, Molecular Nature, Video

Imagine a time when our young Earth was spinning much faster and days were only 8 hours! Our sun was much cooler and less bright than today. There was no oxygen in the atmosphere. Those were the conditions when first photosynthetic organisms with purple pigments evolved in liquid environments. In this animation we see one such ancestral form of early anoxic photosynthesis taking place in the purple bacteria Rhodobacter sphaeroides in which oxygen is not produced. Life evolved into oxygen […]

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