Antibiotics PP

Submitted by amprovost on Thu, 04/27/2017 - 12:20

            This experiment was performed by doing two things with a soil suspension. First, the suspension was streaked onto a casein-starch plate. Second, this suspension was diluted by taking one milliliter of suspension and transferring it into nine milliliters of sterile saline. This new solution was then also streaked onto a separate casein-starch plate. After the Streptomyces were isolated, three individual colonies were taken and streaked in a heavy band across the top quarter of an antibiotic-test plate. These heavy bands were then cross-streaked with S. aureus, E. faecalis, K. pneumoniae, and A. hydrophila. A control plate with all of these organisms and no Streptomyces, to show what uninhibited growth would look like. After allowing these organisms to grow, there appeared to be no inhibition by Streptomyces, as the cross-streaked organisms grew perfectly across the entire area inoculated, looking quite similar to the streaks in the control. One possible explanation for this is that Streptomyces does not produce any antibiotics that affect these types of organisms. Another possible explanation for this is simply that the Streptomyces were not given enough time to produce antibiotics, and perhaps the expected results would have been displayed had the plates been left undisturbed for a longer period of time.

Nitrogen PP

Submitted by amprovost on Thu, 04/27/2017 - 11:52

This graph shows that the expected results were confirmed in regards to growth, as the plant inoculated with bacteria and given nitrogenous fertilizer grew to be the tallest. The plant with nitrogenous fertilizer and bacteria also grew eleven nodules, the plant with only bacteria grew thirty nodules, the other two plants grew zero nodules. This does not confirm the original prediction as the plant with bacteria and no nitrogenous fertilizer still grew nodules, which are usually present when the organisms live in symbiosis and the bacteria fix nitrogen in the soil. A possible explanation for this result is contamination with nitrogenous fertilizer, as it is possible somewhere in the experiment the plant was either fertilized with the wrong fertilizer or with a tool contaminated with nitrogenous fertilizer.

journal

Submitted by jiadam on Thu, 04/27/2017 - 10:53

Introduction:

Bryophytes are a very diverse phylum containing approximately 12,000 different species. With such diversity comes a variety of ranges moss can live in (Lepp). These species participate in ecological interactions, such as mutualism, commensalism, or competition, with one another and with other plant and animal species, living in close proximity (Smith et al.). Moss species shape the environment they live in and, conversely, the environment shapes their growth and survival (Katschnig et al.). Thus, a critical point of study is how bryophyte diversity relates to the abiotic conditions of an environment (Isermann).

The project aims to explore the species diversity in bryophytes and identify how temperature and humidity affect the diversity present on the UMass Campus, a rural  setting. These factors were chosen because of the agricultural implications we can learn from studying the model organism like bryophytes. By looking at the differences in moss over a week span, it shows that the humidity and temperature inside and outside are truly important factors when it comes to diversity and abundance.

Project 3 starting ground

Submitted by abnguyen on Thu, 04/27/2017 - 08:49
  • PD1 background

  • T-cell activation background:

    • CD28/B7

    • MHC/TCR

    • Suppressors of this (CTLA4)

  • Tumor infiltrating cells: how to select for them, advantages to using them

 

  • Prior drugs downfalls targeting the same stuff

 

GOALS:

  • Edit patient white blood cells using CRISPR to:

    • knock out PD-1

    • CD28 superagonist that won’t cause organ failure????

  • T cell activation and deactivation

    • Keep T cells constitutively active

  • Find antigens specific to non small cell lung cancer

“Immune system ablation - getting rid of the regulatory t cells and myeloid something suppressor cells - engineer the tcells to be unresponsive to those suppressive effects: another advantage to hyperactivated t-cells, you better make sure those t-cells only target specific neoantigens to prevent autoimmune disorders - must only target t-cells that exclusively bind to antigens on the tumor :D  “ - randy

 

Keytruda® is a highly selective humanized monoclonal IgG4 antibody directed against the PD-1 receptor on the cell surface. The drug blocks the PD-1 receptor, preventing binding and activation of PD-L1 and PD-L2. This mechanism causes the activation of T-cell mediated immune responses against tumor cells.

 

T-cell activation:

https://www.thermofisher.com/us/en/home/life-science/cell-analysis/cell-analysis-learning-center/cell-analysis-resource-library/ebioscience-resources/t-cell-activation-functional-assay.html

History of T cells of the past 25 years

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2740335/

 

Upregulation of EGFR is one of the main suspects that inhibit immune response.  

    Erlotinib, Tagrisso from project 1

https://www.nature.com/news/first-crispr-clinical-trial-gets-green-light-from-us-panel-1.20137

  • CRISPR

http://biosky.co/clinical-trial-using-crispr-edited-white-blood-cells-to-treat-lung-cancer/

  • More CRISPR

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730182/

More and More CRISPR

 

Deep Brain Stimulation

Submitted by johanthomas on Thu, 04/27/2017 - 00:11

Deep brain stimulation (DBS) is a therapy used to treat a variety of diseases including Parkinson's, OCD, depression, and even chronic pain. It's a surgical procedure implanting electrodes into the brain in optimized areas to reduce symptoms of disease. As with any brain surgery, there is a very serious risk of complications occuring after the procedure.

DBS works by blocking electrical signals in the overactive areas of the brain where the electrodes are placed. The system is called a neurostimulator: a battery operated device that can deliver the electrical stimulation. The battery is also implanted subcutaneously usually under the collar bone or in the abdomen.

Nitrogen Fixation

Submitted by amprovost on Wed, 04/26/2017 - 23:37

I was recently part of a team that studied how microbes cycle nitrogen in their environment. Our findings were as follows:

This lab had four different experiments performed regarding fixation, ammonification, nitrification, and denitrification.

            In the fixation experiment, it was expected that the plant with both nitrogenous fertilizer and bacterial inoculant would form nodules along its roots and grow better than the other three plants, as the nitrogen fixing bacteria would form a symbiosis with the plants. The results are displayed in the following graph.

 

This graph shows that the expected results were confirmed in regards to growth, as the plant inoculated with bacteria and given nitrogenous fertilizer grew to be the tallest. The plant with nitrogenous fertilizer and bacteria also grew 11 nodules, and the plant with only bacteria grew 30 nodules, the other two plants grew 0 nodules. This does not confirm the original prediction as the plant with bacteria and no nitrogenous fertilizer still grew nodules, which are present when the organisms live in symbiosis and the bacteria fix nitrogen in the soil. A possible explanation for this result is contamination with nitrogenous fertilizer, as it is possible somewhere in the experiment the plant was either fertilized with the wrong fertilizer or with a tool contaminated with nitrogenous fertilizer.

            In the ammonification experiment, three flasks were utilized. One flask contained rich soil, one flask contained poor soil, and one flask contained P. vulgaris. It was predicted that the flask containing bacteria would show the lowest levels of ammonia as this organism can break down ammonia. The ammonia levels in the flasks were tested using quantofix ammonia test strips. The results can be seen in the following graph.

The expected results were confirmed by this experiment, as P. Vulgaris had the lowest ammonia levels at the end of the experiment.

            In the nitrification experiment, it was predicted that the rich tubes would show a larger decrease in ammonia and increase in nitrate, as the rich soil would have more ammonia to convert to nitrite or nitrate. The results of this experiment are displayed in the following charts.

 

ASB Data

Week

Poor Soil Ammonia

Rich Soil Ammonia

Poor Soil Nitrite/Nitrate

Rich Soil Nitrite/Nitrate

1

0

0

0

0

2

0

0

10 mg/L NO3- & 1 mg/L NO2-

 

10 mg/L NO3- & 1 mg/L NO2-

 

3

0

0

10 mg/L NO3- & 1 mg/L NO2-

 

250 mg/L NO3- & 40 mg/L NO2

 

4

N/A (not enough mixture left to test)

N/A (not enough mixture left to test)

50 mg/L NO3- & 10 mg/L NO2-

 

500 mg/L NO3- & 80 mg/L NO2-

 

 

NIB Data

Week

Poor Soil Ammonia

Rich Soil Ammonia

Poor Soil Nitrite/Nitrate

Rich Soil Nitrite/Nitrate

1

N/A (not recorded by partner)

0

0

0

2

N/A (not recorded by partner)

0

10 mg/L NO3- & 1 mg/L NO2-

 

10 mg/L NO3- & 1 mg/L NO2-

 

3

N/A (not recorded by partner)

0

100 mg/L NO3- & 1 mg/L NO2-

 

25 mg/L NO3- & 40 mg/L NO2

 

4

N/A (not recorded by partner)

N/A (not enough mixture left to test)

50 mg/L NO3- & 10 mg/L NO2-

 

500 mg/L NO3- & 80 mg/L NO2-

 

 

            The fluctuation in levels of nitrite and nitrate can most likely be attributed to denitrifying bacteria. Denitrifying bacteria can reduce nitrite and nitrate into gaseous compounds, which may have escaped the flasks. No data was recorded on the levels of ammonia in the NIB poor soil by my partners in charge of this experiment, hence the lack of reporting on this section of the chart. The expected results were confirmed, as the rich soils produced more nitrite and nitrate than the poor ones.

            In the denitrifying experiment, four different tubes of nitrate broth were used, one containing P. vulgaris, one containing P. aeruginosa, one containing rich soil, and one containing poor soil. The expected result was that it one would be able to determine the presence or lack of nitrite and nitrate in the broths using nitrate reagent A, nitrate reagent B, and zinc. After applying nitrate reagents A and B, a red color change indicated that nitrite was present. If there was no color change, zinc was added, if there was still no color change, this indicated that nitrate was broken down into a compound other than nitrite. If a red color change occurred after being exposed to zinc, this meant that nitrate was still present and never denitrified. The NB rich soil had nitrate break down into compounds other than nitrite. Both the NB poor soil and the P. vulgaris had the presence of nitrite. The sample with P. aeruginosa had nitrate broken down into compounds other than nitrite. The expected results were confirmed, as it was possible to determine the presence of nitrite or nitrate using these tests.

Plant Diversity Poster Sections Draft

Submitted by dkotorobay on Wed, 04/26/2017 - 23:34

 

Overview:

Plants that exhibit pronounced water storage in one or more organs are generally classified as succulents. There are other characteristics that ensure the plants survival in a water limited environment, this is referred to as “the succulent syndrome”. Hallmark traits of this “syndrome” includes a shallow root system that allows for the rapid uptake of the unexpected rains that are common in deserts; a thick waxy cuticle that prevents excessive water loss, and CAM photosynthesis, which allows plants to uptake atmospheric carbon dioxide at night when water loss is reduced.

Background:

Euphorbia milii are native to the island of Madagascar. It is has a woody stem and that is adapted for water storage, it has red inflorescences that are found in clusters called cyathiums. It also produces a poisonous milky sap. 

Euphorbia and Aizoaceae:

The Aizoaceae are a type of old world succulents. The leaves and stems are fleshy and close to the ground and it relies on CAM photosynthesis. The Aizoaceae are a flower producing succulent though the flowers are not produced consistently, there are no spines for protection. 

Euphorbia and Cactaceae:

The Cactaceae are a large and diverse group of stem succulents that are predominantly found in the arid environments of the North and South Americas, they are a combination of old and new world succulents. They have a fleshy stem as opposed to the woody stem of the Euphorbia, but there are spines present, different than those of the Euphorbia milii because the spine on Cacti are modified leaves. Cactaceae also produces flowers or inflorescences on the ends of the growing tips. 

Euphorbia and Didiereaceae:

The Didiereaceae is a new world type of succulent. Euphorbia milii and the Didiereaceae are both found in Madagascar and are the most similar morphologically. The Didiereaceae also has a woody stem with long spines, the way that they differ is the leaves are right next to the spines and there is leaf growth throughout the stem, and there are no inflorescences.

*The Madagascar lemurs climb the Didiereaceae and eat the leaves off the stems.*

Nutrients

Submitted by scestero on Wed, 04/26/2017 - 23:32

BEfore the mass exxtinction in the late Quartenary, massive mammals roamed the earth and its seas. These animlas are predicted to be up to 50% larger than their current forms. For example the blue whale is only a fraction of the size its ancestors were back then and the bluw whale is the largest mammal on earth currently. People often neglect studying the ecosystem once a species has gone extinct. After theQuarternary there was a huge probelm with nutrient flow, specifically P, N and Fe. IN the case of P, it can be transported well by sea animals. Whales can pick up P from the ocean floor and disperse it during itss migarations. they can also disperse the P vertally in the ocean, allowing for seabirds to take advantage of this. Salmon and other anadramous fish play a huge role in P dispersal, even more so than sea birds. These fish will swim from oceans to rivers and streams and hten back into the ocean. This carries the P to land and allows for terrestrial aniamls to disperse ut on land. Salmon will carry the P up rivers and bears that eat the fish will spread it onto land. 

journal

Submitted by jiadam on Wed, 04/26/2017 - 15:52

Pre-rc

The pre-replication is a 6 subunit heterohexamer at the origin of replication which is the start point of replication. Because replication occurs bi-directionally, two replication fork go into separate directions to speed up the replication process. Budding yeast only have 16 chromosomes and around 300 origins. Humans have around 6 billion base pairs of DNA and need much more origins of replication to get replication done in a quick manner. As soon as the first origin of replication is fire, the cell is in S phase. Origins can fire at different times. Some fire early in S phase and others fire later towards the end of s phase. In each replication fork, each strand is a template for a newly synthesized strand and the polymerases that are replicating the DNA are physically connected.

 

Mechanism of DNA rep

Submitted by sjurgilewicz on Wed, 04/26/2017 - 13:26

Replication starts at the origins of replication. The pre-RC is made of 6 subunit heterohexamer found at the origins of replication. Replication happens bi-directionally, two replication forks go in different directions. Humans have 6 billion base pairs of DNA with many origin of replications to have replication happen in a timely manner. Origin firing is where replication starts, some fire early in S phase while others fire in late S phase. Each strand of DNA is used as a template and a new strand is synthesized from 5’ to 3’. The new nucleotide is added at the 3’ end to the previous nucleotide. DNA polymerase cannot make a strand without a previous nucleotide to add to with the free 3’ OH group. Primase adds an RNA primer that is complementary to the template strand of DNA, which supplies the 3’ end for the DNA to build off of. The incoming nucleotide is a triphosphate, which supplies energy for the reaction. A pyrophosphate is released and gets recycled when the bases pair. The H from the 3’ OH is removed and a bond is formed between this oxygen and the previous 3’ OH. This is call a phosphodiester bond. The leading strand can be synthesized continuously, but the lagging strand is replicated in pieces called Okazaki fragments. DNA polymerase cant attach the fragments, so DNA ligase seals the gap.

The lagging strand loops back on itself, 180 degrees, which allows for the same direction synthesis as the leading strand. There are specific proteins present during replication, helicase (pulls apart DNA), DNA polymerase, sliding clamp (keeps DNA pol. from falling off of DNA so replication can continue) and sliding clamp loader.

Pages

Subscribe to Writing in Biology RSS