You are here

danielcosta's blog

Epigenetics

Submitted by danielcosta on Fri, 11/10/2017 - 02:02

Epigenetics is the study of changes in gene function that are not caused by changes in the DNA sequence. This is a quite interesting and rapidly growing field of genetics. Epigenetics describes phenomena in which genetically identical cells may express their genomes differently, which will cause phenotypic, or observable, differences. The driving forces of epigenetic differences are mainly environmental effects. The two main components of epigenetic code are DNA methylation and histone modification. DNA methylation is when methyl marks are added to certain bases of the DNA. This can repress gene activity of the methylated DNA. Histone modification is the process by which a combination of different molecules may attach to the end of a histone's "tails". This may alter the gene activity of the entire strand of DNA wrapped around the histone. 

Open Channel Waterflow

Submitted by danielcosta on Wed, 11/08/2017 - 22:15

There are three categories used to broadly define the energy status of flowing water in an open channel system. The slowest flow is defined as subcritical flow. This energy status is represented by slow moving water that is moving laminarly, or in parallel in relation to the water around it. The fastest flow is defined as supercritical flow. Water in this category is moving in a turbulent manner; parcels of water are mixing with each other and there is no uniform direction of waterflow. The transition zone, the zone of energy where subcritical flow transitions to supercritical flow, is defined as the critical zone. In this zone, water gains momentum and speed and begins the process of becoming less uniform. A physical example of the three categories of flow is well represented by a waterfall. At the top of the fall, before the drop, there is the subcritical flow, in which water is moving relatively uniform in a laminar manner. Here, the water seems to be moving relatively calmly, as gravity is the only driving force of flow. Once water reaches the edge of the drop, it begins its ascend to the bed below it and becomes slightly turbulent. After the water reaches the bedrock below, there is no uniform flow at all, as the water is now fully turbulent. Flow here is dominated by inertia and moves in any which direction with brute force. 

Cell Death

Submitted by danielcosta on Mon, 11/06/2017 - 22:53

Cell death is an important process in plants. It can be brought about for various reasons including pathogen-resistance and plant development. There are three types of cell death in plants. There is programmed cell death which includes apoptosis and autophagy, and there is nonprogrammed cell death which includes necrosis. Programmed cell death is an active process that is utilized to rid the plant of damaged or unneeded cells. During apoptosis, chromatin condensation and DNA fragmentation occur and cytoplasmic components enter the vacuole, where lytic enzymes breakdown the now useless material. During autophagy, the vacuole of the plant cell is ruptured and the lytic enzymes breakdown the organelles and cytoplasm of the cell. We have not learned about unprogrammed cell death yet and so I cannot accurately describe this to you at this time. 

Dissecting a Spiny Dogfish

Submitted by danielcosta on Thu, 11/02/2017 - 20:08

Yesterday in lab, students were tasked with skinning and dissecting a spiny dogfish specimen. In order to do this, incisions were made on the dorsal and ventral side of the dogfish. The dorsal incision should have been made from the second dorsal fin to the top of the skull. The ventral incision should have been made from the anus to the corner of the mouth. This part was challenging because the goal was to skin the dogfish in a way that left all muscle underlying the skin intact. If students made their insicions too deep, the muscle would be cut, and the skinning process would rip the muscle out as well. Once the dorsal and ventral incisions were completed, two more incisions along the side of the specimen was to be made. The purpose of this was to connect the dorsal and ventral incisions in order for the dogfish to be skinned. Once the specimen was skinned, its muscles were clearly visible. This lab procedure was carried out by students in order for them to study the muscles of the dogfish. Next week, students will be tasked with further dissecting their dogfish specimen, going past the muscle and reaching the organs. 

Riparian Areas

Submitted by danielcosta on Tue, 10/31/2017 - 14:31

Riparian areas are one of the most essential elements for a clean, efficient watershed system. The major purpose of a riparian area is to filter out sediment and nutrients that would otherwise runoff into streams, rivers, lakes, ponds, and other water systems. There are three components to a riparian area, which are otherwise known as "Zones". They are differentiated by their proximity to the body of water they protect and each has a specific function. The closest zone should be about 15-25 feet wide and should contain herbacious shrubs that thrive well in wet conditions. The middle zone functions best when it is 50 or more feet wide and should contain a variety of trees that grow tall. This may be the most important zone as this vegetaiton will act to not only grow tall and shade the water, but also use up a majority of the insoluble nutrients that would runoff into the water. The last zone functions as the primary barrier between the surrounding land and the body of water. This mostly-grass-filled area will help to prevent overflowing of the water system in the event of heavy storms. This last zone can be an area in which livestock roam and graze. The importance of riparian areas should not go overlooked, as it is the key component in the difference between a healthy watershed system and a watershed system that is not even habitable.

Carps and Minnows

Submitted by danielcosta on Mon, 10/23/2017 - 17:54

Of all the fishes that are to be examined for my Ichthyology Lab pracitical, the carps and minoows are by far the hardest group of fishes to distinguish the species from one another. Unlike other families and groups of fishes, the carps and minnows have only the subtlest of physical features that may determine one species from another. For example, where I may be able to determine a Burbot from an Atlantic Tomcod based on the presence of 2 or 3 dorsal fins, I would only be able to determine a Golden Shiner from a Rudd based upon the number of scales that appear dorsally to the lateral line of the individual. These subtle characteristics of the carps and minnows could increase the difficulty of the lab practical tremendously depending on how many different carp and minnow species are put out for examination.

methods abstract

Submitted by danielcosta on Thu, 10/05/2017 - 22:08

    In order to develop skills in scientific writing and multi-panel scientific figure creation, students were tasked with locating a species of their choice, photographing said species, creating a multi-panel scientific figure using their unique photographs, and creating a set of methods explicitly detailing their exact procedure. They were to exchange their methods with another student and follow their partner’s methods as precisely as possible in order to create a replicate figure. The two figures were to be observed for differences.

   My original and replicate figures turned out to be significantly different but also contain some easily observable similarities. The differences lay in the perspective of the images taken, lighting of the images, usage of Google Maps in showing my species’ location, and sizing of several components of each figure. With human error always a factor, many differences are to be expected. These results point to inconsistencies in the way the methods were both described and followed as well as the manner in which certain aspects of the methods were interpreted. The brief amount of similarities point to a few concise descriptions in the methods section that are easily repeatable.

icthyology notes

Submitted by danielcosta on Wed, 10/04/2017 - 16:56

The phylogeny of early fishes is fairly simple. It all began with the evolution of vertebrates. From here, all fishes that we know of today are derived. The earliest group of fishes are known as the Agnatha. These fishes were jawless, and are more commonly known as the cyclostomata. After some time, jaws began to develop. This is where the next extremely broad group of fishes began to evolve. The gnathostomata, or jawed vertebrates, contain four major divisons: Placodermii (extinct), Chondrichthyes, Acanthodii (extinct), and Osteichthyes. The two groups that currently inhabit the Earth make up all of the fish diversity aside from the two groups of Agnathan fish still alive. The Chondrichthyes are a group of fishes that are entirely made up of cartilagenous skeleton. On the other hand, the Osteichthyes are a group of fishes whose skeletons are made up of bone. The Osteichthyes contain the majority of fish diversity worldwide, totalling about 95% of all diversity. This is the beginning and most simple cladistic splits of fishes. 

salt-tolerance in Arabidopsis

Submitted by danielcosta on Tue, 10/03/2017 - 21:31

Salinity levels in soil is a major factor in the limitation of crop yields. Wordwide, about 30% of all irrigated crops are affected by high salinity levels. Presence of excess NaCl molecules in plants impede water uptake as well as reduces photosynthetic rates. This will lead to energy depletion and accumulation of reactive agents inside the plant's cells. Plants attempt to cope with this water loss by closing their stomata and compartmentalizing intracellular Na+ through the use of vacuoles. However, the ways in which salt-tolerant plants maintain energy levels and re-allocate limited resources is not well understood.

A proposed pathway of salt-tolerance in plants is that of macroautophagy. Autophagy maintains cellular homeostasis by enclosing unwanted molecules or damaged organelles in a double-membraned vesicle that becomes what is known as an autophagosome. An autophagosome fuses with the lytic vacuole in order for its contents to be destroyed and/or recycled back into the cell. There are a few autophagy-specific proteins that are key in driving the formation and expansion of autophagosomes.

In order to test the hypothesis that a high autophagic flux positively correlates with salt tolerance in Arabidopsis, mutants defective in autophagic processes and mutants with reduced levels as well as transgenic plants with increased autophagy levels were selected by researchers for analysis. They concluded their findings by summarizing that autophagic flux is rapidly induced by salt treatment. They also state that their physiological analyses revealed that mutants accumulated less sugars and proline, or osmolytes that play a role in maintaining cell volume and fluid balance, while the transgenic plants accumulated more. Their observations suggest that salt stress leads to autophagy in order to facilitate bulk protein turnover which provides the macromolecules and energy required for the plant to survive. In short, autophagy is they key factor in salt tolerance in Arabidopsis. 

differences

Submitted by danielcosta on Fri, 09/29/2017 - 14:27

1. FACTORS

      a. camera position/zoom

      b. weather

      c. figure set-up

      d. google map orientation

      e. graph set-up

2. Controllable vs. Non-Controllable factors

      a. controllable: camera angle/position/zoom, figure set-up, google map usage, graph set-up, data

      b. non-controllable: weather

3. Observations

      a. original figure

  • taken on a sunny day
  • close-up pic
  • google map image from directly above
  • google map image contains labels and location marker for species photographed
  • no tic marks or axid boundaries on graph
  • graph: Campus Pond- 1000ft, N. Village Dr Pond- about 3650ft, Sylvan Pond- about 4050ft
  • all panels of figure contains identification in lower case black lettering

      b. Replicate Figure

  • taken on overcast day
  • camera not too close to the species in question
  • camera angled in a position you can see buildings and trees in background
  • google map imaghe taken at an angle, not looking straight down
  • google map image is positioned from behind the Mullins Center
  • graph contains tic marks ands axis boundaries
  • figure panel identification is not consistent
  • graph: Campus Pond- 1000ft, N Village Pond- 3500 ft, Sylvan Pond- about 3900ft

Pages

Subscribe to RSS - danielcosta's blog