Nov 03, 2019
The term clade is used in biology to describe a group of organisms which are related by sharing a common ancestor. Moreover, part of the definition of clade requires that the group of organisms be complete: all descendants of the common ancestor must be included.
Clades can be and typically are nested inside each other.
Clades serve as a basic unit in biological taxonomy. Large groupings of organisms such as taxa are required, ideally, to be clades.
Nucleic Acid Design
Sep 09, 2019
Suppose you want to create a biomolecule using nucleic acid sequences (e.g., GCACGAGT). How do you go about doing this? Nucleic acid design involves creating a set of sequences which will then combine into the desired biomolecule. Those interested in accomplishing such a feat are typically working in the fields of DNA computing or DNA nanotechnology.
Constructing a biomolecule with the desired structure using nucleic acid sequences is easier than making a protein (also a biomolecule).
Jun 01, 2019
The Ruzzo-Tompa algorithm is a method for finding distinct subsequences in a sequence of numbers such that the sum of the subsequences reaches a maximum. The difficult part here is ensuring that the subsequences are distinct and non-overlapping.
Consider the following sequence: \((1, 2, 3, -5, 1, 2, 3)\). While one might be tempted to extract the two subsequences \((1, 2, 3)\) and \((1, 2, 3)\), skipping over the -5, the two subsequences are not distinct.
May 14, 2019
FASTA is a text-based format for storing data about nucleotide or amino acid sequences. Each nucleotide or amino acid is represented by a single ASCII letter.
Sequences can be stored in a text file in FASTA format in the following way. A line beginning with > indicates that the sequence will start on the following line. (The line with the > may contain a name or unique identifier for the sequence.
May 11, 2019
Nanopore sequencing is a method of sequencing DNA and RNA. It is a technology which is positioned to replace (or supplement) sequencing using the polymerase chain reaction (PCR). (PCR was developed in the 1980s.) Nanopore sequencing is potentially cheaper than sequencing using PCR. Nanopore sequencing uses an electric field to move a sample through a nanopore, a pore of nanometer size. When the sample gets close enough to the nanopore, one can gather information about the sample by looking at changes in electric current density around the nanopore.
Apr 21, 2019
Vito Volterra was an Italian mathematician and physicist (1860–1940). He was born in Anconda, a port city in central Italy. His name is familiar today, especially to biology and ecology students, because it appears in the name of the best-known predatory-prey model, the Lokta-Volterra model. Volterra came up with the model (independently from Lokta) in the context of studying fish catches in the Adriatic Sea.
Volterra is also remarkable in that he was one of the few professors who opposed the Fascist regime of Benito Mussolini.
Apr 02, 2019
A lipid is a molecule present in biological organisms. If you have heard the term “lipid” before, you might think that it’s synonymous with “fats”. Fats are, however, triglycerides, a proper subset of lipids. What unites lipids is their solubility in nonpolar solvents.
Fatty acids are an important category of lipids. Soaps used in cleaning and bathing are made from fatty acids. Triglycerides, mentioned already, are another significant category of lipids.
Modeling DNA Evolution
Mar 17, 2019
Suppose we gather the entire DNA sequence from organisms of the same species once a year for 1,000 years. If we count the frequency of bases (C, G, A, T) in each of these sequences we will observe that they are not identical. In some sample sequences C might be higher than in others. In other sequences, G might be more prevalent. Evolutionary biologists are interested in studying and, indeed, formally modeling this variation.