Writing in Biology - Section 1

Palaces were large scale structures commissioned by elites who had some control over the people living on Crete. The elites used 3 strategies to get the Minoan masses to accept their rule. First, benefits included being a part of a group with an impressive and immense structure used for rituals and gatherings and fortifications to towns for protection (Minoans of). Second and third, according to archaeologists, previous religious sites were replaced by the palaces or ‘state’ shrines, which implies the elites may have coerced people into abandoning their previous beliefs and pushed people to adopt a new ideology. These state shrines or palaces were large building complexes with multiple floors and specialized rooms. The elites that lived here enjoyed lavish lifestyles; bathrooms with wooden seats and possible flushing apparatuses leading to the main drainage system (First Aegean). In lower rooms, large ceramic jars indicate palaces were storage facilities used for storing, redistributing, and trading wine and olive oil (Minoans of). Evidence also shows the Minoans were in contact with Egypt, exchanging their cloth, timber, and foodstuffs, for copper, tin, gold, silver, and hippopotamus ivory (Minoans of).

Genomic analysis is the identification, comparison of genetic features and their expression through the use of techniques such as DNA sequencing and bioinformatics. Genomic analysis is generally considered to be divided into two categories; structural genomics which identifies certain genomic structures in the genome and functional genomic analysis which analyses the expression of genes and their interactions often also called transcriptomes. Genomic analysis was made available through the prevalence and availability of gene sequencing. While human genome project sequenced the entire human genome most of the genomic analysis would not be possible would not be possible without the further accessibility of sequencing to the point where currently it is extremely affordable to have a genome sequenced, and other techniques such as next-gen sequencing and whole-genome sequencing that does not depend on the isolation of cells in order to sequence the genes. Because these data that are generated from sequencing are generally put online in databases, these data are both available and able used to be used for purposes that are not intended by the researchers who have originally made the sequence. The data set is so large that a single sequencing can be the basis of several papers. Because of this, there is a data analysis bottleneck where there is so much data that needs to be analyzed but there is not enough time or computing power to analyze the entire genome for all the information that it can yield. Because there are so many different venues that use bioinformatics, there is a major need for people who are able to analyze the data that is available and easily accessible.  Degrees in Bioinformatics is quickly becoming one of the highest-paid and available jobs on the market.

Hox genes are a superfamily of genes that specify an organism’s body plans. Within the protein made by the HOX genes, there is a homeobox domain is a domain that controls anatomical development in eukaryotes. In animals, there are 16 major classes of homeodomains. HOX genes were originally discovered in 1994 in fruit flies. The HOX gene is especially important in the regulation of development. A mutation in the HOX gene can have a crippling effect on the development, often resulting in physical disorganizes or termination of pregnancy. Because HOX genes are most vital to the development of the fetus, the HOX gene is mostly conserved across species. A mutation in HOX gene that gets fixed in a population can result in a completely new plan such as those that are present in snakes. In snakes, they specifically have a mutation in the HOX6 gene which causes the snake to lose the forelimb. Because of this, snakes have a widely different body plan compared to those of its close relatives who have forelimbs. In labs, hox gene regulation and expression can be manipulated to make certain body parts grow where there normally isn’t a certain body part. The most famous example of this is in fruit flies where researchers caused legs to grow where the eyes should be by manipulating a hox gene called antp. Experiments show the importance of HOX gene in maintaining the general structure of the body plan.

Nuclear lamin are a type five intermediate filament in all animal cells that little is known about. It is not common knowledge to know what nuclear lamin are or what they do. However, nuclear lamina mutations are responsible for a high number of common diseases in the human population. Nuclear lamina come in two main types, A and B. Both types of filaments have subtypes, and all animals express at least one subtype of B lamins. A common disease occurs when a type A prelamin, that is a type A lamin that is modified to produce other subtypes of A lamin, has a mutation to not allow it to bind properly to membranes and DNA. It congregates in the nuclear envelop and causes progenic syndromes and muscular dystrophies. These affect many people across the globe and nuclear lamina is clearly very involved in multi-cellular organisms. They are very structurally important for working muscles and an effective nervous system. 

The endoplasmic reticulum makes up 10% of the cell's volume and surounds the nucleus. There are two types of ER: smooth and rough. The smooth ER contains no ribosomes on its membrane, hence the name smooth. This is because the main purpose of the smooth ER is to synthesize lipids and decrease toxicity of the cell. In contrast the rough ER has ribosomes scattered along the membrane because the main purpose of the rough ER is to synthesize, process, and export protiens. In terms of the relationship of the ER to ribosomes, a ribosome will recgonize a translation initation sequence of an mRNA and begin synthesizing the protein. This complex will then bind a tranlocon located on the membrane of the ER. This channel protein will direct the newly synthesized protein into the lumen of the ER. The protein is then processed and can possibly be retained in the lumen, secreted into the cytoplasm, or released in a vesicle. 

The driver of evolutionary change is natural selection, a process where communities thrive or perish depending on the environmental conditions. Despite the unique traits that darwinism has brought, these evolved bodily functions are not exclusive to one species. Lamnid sharks and tunas are an example of two species thought to have independently evolved similar traits. However, there is little data regarding the mechanisms behind their convergent evolution. Under these circumstances, researchers have investigated the evolutionary relationship between mako sharks, Isurus oxyrinchus, and tunas’ swift, continual movement and morphological design. They also compared swimming kinematics, and muscular function to determine this. When exposed to a controlled swim tunnel, scientists observed how both species concentrate movement in their posterior, more specifically, the caudal region of the tail.

Results showed that mechanistically, allowing the mid-body to become virtually stiff and focusing muscle activation in the rear has evolutionarily allowed these fish to become more energy efficient. Because the tuna and shark resemble one another in their structural design, both are able to swim for longer periods of time compared to other fish, without the cost of travel. The important feature in tunas which allow this specialized movement is the physical uncoupling of the red and white muscle when in motion. In other species, the muscles act synchronously. This thunniform-like mobility in tuna was tested for similarity in mako shark via sonomicrometry, by shortening the muscle during passive and active swimming in the hopes to detect uncoupling. Throughout active swimming, they recorded asymmetrical muscle activity. There was a delay in red muscle strain compared to white muscle. This confirmed that red muscle was in fact uncoupled, supporting the claim that tunas and mako’s are evolutionarily similar. This is also indicative of strong posterior movement. The analogous relationship between the two species was supported morphologically as well. Elongated tendons were measured in both fish. Its association with the red muscle creates a system which allows the transfer of great power from the anterior of the animals’ to the posterior.

However, the driving force behind the system was found in the hypaxial lateral tendons in sharks, whereas the tuna’s primary source of transmission is located in the horizontal septum of the tendon. Despite this regional difference, the study overall was representative of a phenomenal evolutionary relationship between two separate species; though it does have its complications. Studying animals such as sharks without sedation can serve to be quite difficult. These predators pose great danger to the handlers, so precautions must be taken and some methods may be carried out quickly; resulting in fewer studies and limiting the amount of information available to others. To avoid potential risks in the future, studying the similar, less harmful tuna in the place of lamnidae can be useful.

A future experiment may include a common ancestor of the tuna to study the mechanisms in which they diverged. This will help map out the history of how tunas were able to develop different characteristics over time, and eventually become similar to the mako shark.

Gene duplication is a mechanism where genetic material is essentially generated and copied in a region of DNA. A regulatory mutation is a mutation that affects the spatial or temporal regulation of the gene without causing an entire loss of the gene product. Lastly, coding sequence mutations are changes in the coding sequence that can have different outcomes in expressivity like nonsense or missense mutations.

These three factors combined aided the use of a snake's venom to evolve into what it is today: from defensin genes that are used for different basic tasks like fighting infections in the pancreas, to today’s cromatine genes that encode the venom molecules and are used for attacking and destroying muscles. These changes did not alter the universal product of the gene, but in turn changed the way the genes were communicating. By sequencing genes from different snakes and mapping them out in an evolutionary tree, scientist Fry, colleagues compared the relationship of defensive and cromatine genes and found out that they are closely related. In newer generations that inherited the defensive gene, gene duplication took place for this change to occur.

There may have been an accidental duplication of a gene in which in turn would spark a new gene recruitment. Regulatory gene mutations would occur because gene recruitment now took place, helping change the gene’s functions through mutations: one of these copies would now be able to produce proteins in a venom gland. At the DNA level, a type of mutation could have occurred at the coding sequence by changing the amino acids, which, for this example, could have changed the expression of a gene from being a defensin gene to cromatine even by one difference in sequencing. Having these factors repeatedly happen over and over again in snakes eventually gave rise to a new family of venom producing genes.

Gene duplication, regulatory mutations, and the coding sequence all play different but important roles in the evolution of venom. Gene duplication, which is a mechanism where genetic material is generated/duplicated, and this area of DNA contains a gene. This event allows one copy to continue with the original function of said gene, while the other copy has the ability to evolve into something else. A regulatory mutation affects the temporal or spatial regulation without causing a complete loss of the gene product. This basically means that the mutation can change the different tissues the gene is expressed in, without losing the purpose/function of the gene itself. A coding sequence mutation is when a base is changed within the amino acid, and this can cause either a nonsense or a missense mutation (can change the whole amino acid or just the base).

Gene duplication plays a role in the evolution of crotamine because after the defensins evolved from a common ancestor and was inherited between many animals, including snakes, the extra copies of this gene created by gene duplication allowed the defensins to become more specialized. In the case of these snakes, the specialization was for attacking different pathogens found in the pancreas. This duplication, according to Fry, began to change the actual shape of the protein (after many duplications). A new shape meant a new function, which leads us from defensins to crotamine. The regulatory mutation changed the location of where the protein was being produced (from the pancreas, to the mouth). This mutation played a huge role in the usage of this gene. With a gene that damaged muscles instead of pathogens, found in a place crucial for killing prey it could easily used to incapacitate and kill the desired prey. As for the coding sequence mutation, a simple change of one amino acid could cause a cascade of other elements that led to crotamine as a deadly, venomous, protein. This type of mutation could explain how ancient venom is, especially in certain snakes that are deemed non poisonous. Meaning that a coding sequence mutation could’ve caused earlier ancestors to produce crotamine. This, along with gene duplication and regulatory mutation, played big roles in the evolution of crotamine, from defensins.

A variety of mechanisms allow fish to propel themselves through an ever-changing environment. Locomotor techniques such as wave-like motions are currently being researched, and with the help of recent technological advances, can now be examined in greater detail. In this article, George V. Lauder of Harvard University observed how morphological differences in fish, and the basic commonalities of swimming has become better understood. He viewed new approaches in kinematics, hydromatics and robotic studies of undulatory fish.

Lauder emphasized that not all fish use their fins the same way, because variations in their body shape make them complex. Stingrays are a unique example of this. Their flexible bodies and expanded pectoral fins help increase amplitude and lift. A study Lauder reviewed about center of mass dynamics (COM) went further in detail. Scientists compared a bluegill, clown knifefish, and an eel during surge and sway-like undulatory motion. The results from this study revealed that sway increased as speed increased. Researchers also observed that sway displacement was largest in eels. Lauder expressed that this particular experiment on COM was vital for understanding how physique affects aquatic propulsion, especially because COM research is lacking. He also notes that fish are able to alter the surface area of their fins. This helps them maneuver through difficult areas. In addition to kinematics, Lauder discussed a shark study which implemented a new hydromatic strategy by using 3D reconstructions of bonnethead sharks.

The experiment tested whether shark skin denticles have an effect on performance. Scientists 3D printed two bonnethead sharks, with and without denticles. When placed under appropriate swimming conditions, they discovered that intact surface skin increased the shark’s speed by 12.3%. This suggested that denticles can reduce drag, therefore improving performance. Biomimetics are an alternative to studying animals like the sharks in this study, because it is both harmless and safe for all that are involved.

Consequently, this has lead scientists to widen their range of research with recent advances in fish robotics. These realistic representations help researchers learn more about fish dynamics in an interactive way. Scientists manipulate variables, and even expose mimetic fish to several different conditions, without the limitations that might occur using live fish. Lauder analyzed an experiment which focused on modifying robotic fin supports to determine which level of stiffness corresponded with maximum performance.

Based on the results, the scientists in this study confirmed that a complex relationship between stiffness and flapping existed. As it turned out, optimal stiffness is based on the frequency of flapping. Constantly altering the shape of their fins allows fish to relax or stiffen their flippers and yield maximum performance with many different speeds. Despite the benefits, Lauder noted that physical models are still imitations and do not yet fully replicate the animals they represent. Even so, employing robotics in research is a safe and favorable alternative for animals that might be harmed for the sake of research. Evidently, these new techniques are incredibly helpful for understanding fish biology and provide innumerable opportunities for future research.