Alx1 Gene Related to Evolution of Larval Skeleton

Submitted by jgirgis on Fri, 04/28/2017 - 11:09

In the study titled “Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton” by Hiroyuki Koga, the alx1 gene was proven to be necessary for the acquisition of the larval skeleton. It also was proven to play a vital role in the evolution of the larval skeleton (Koga, 2016). Echinoderm larvae were the model organisms used to see if alx1 is a necessary gene for the attainment of larval skeleton. Scientists pinpointed Alx1 to see if this gene was necessary for the evolution of the larval skeleton by inducing the expression of alx1 in starfish that do not have a skeleton. To induce the expression of alx1 in starfish, Koga and his team inserted mRNA that coded for Alx1 into the eggs of the starfish through microinjection (Koga, 2016). The goal was to increase the cell numbers of skeletogenic cells. In addition, green fluorescent protein was inserted into starfish embryos, specifically the nuclei to mark the skeletogenic cells.

References:

1. Koga, Hiroyuki, Haruka Fujitani, Yoshiaki Morino, Norio Miyamoto, Jun Tsuchimoto, Tomoko F. Shibata, Masafumi Nozawa, Shuji Shigenobu, Atsushi Ogura, Kazunori Tachibana, Masato Kiyomoto, Shonan Amemiya, and Hiroshi Wada. "Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton." PLoS ONE. Public Library of Science, 11 Feb. 2016. Web. 24 Apr. 2017.

Global Climate Change cont.

Submitted by kmichaud on Fri, 04/28/2017 - 10:47

The most convincing evidence to support the already clear dramatic increase in greenhouse gases and global temperature in the last two centuries involves the Suess Effect. Fossil fuels are formed by the ancient decomposition of organic matter, which is predominantly from vegetation. Elemental carbon, 12C has two persisting radioactive isomers, 13C and 14C, which decay at known constant rates. In modern day plant metabolism, 14C in 14CO2 persists in the environment because its half is approximately 5,700 years. If the atmospheric carbon is produced by modern day respiration, then we would expect the concentration of 14C to 13C to remain stable over time. This has not been the case, as the ratio of 13C to 14C has significantly increased during the time of industrialization. This increase is a result of the use of ancient carbon in fossil fuels releasing more 13C into the atmosphere, conclusively proving that anthropogenic causes are responsible for increased rates of global climate change. 

From Global Climate Change

Submitted by kmichaud on Fri, 04/28/2017 - 10:04

The causes of global climate change and rapid climate warming have been a topic of significant political debate. This debate is largely one sided in the scientific community, as it is widely accepted that the recent rapid increase in atmospheric CO2 emissions and other greenhouse gases is a result of anthropogenic causes. Greenhouse gases, i.e. CO2, CH4 and N2O, are capable of absorbing infrared radiation radiated into space from the Earth’s surface. These gases do not absorb visible light, allowing visible light to reach Earth’s surface and be absorbed by the surface. This energy is then reflected as infrared radiation, which is captured by the absorbing atmospheric gases, resulting in a warming effect. Overall warming is in an unfortunate, positive feedback loop with melting polar icecaps as frozen areas have higher albedo resulting in less absorption of light. As the climate warms, icecaps will continue to decrease in area, resulting in a lower albedo and increased absorption of energy by land masses and increasing global temperatures. 

SOX9 Gene

Submitted by jgirgis on Fri, 04/28/2017 - 09:53

The malformations and syndromes associated with the SOX9 gene include acampomelic campomelic dysplasia, campomelic dysplasia with autosomal sex reversal, and campomelic dysplasia. Campomelic dysplasia and acampomelic campomelic dysplasia with or without sex reversal are caused by a heterozygous on chromosome 17q24.1 Campomelic dysplasia is an autosomal dominant skeletal dysplasia. The malformations include congenital shortness and bowing of long tubular bones, especially in lower extremities.1 Other malformations include narrow iliac wings and nonmineralized thoracis pedicles.1 Patients that have campomelic dysplasia often die within the first year of being diagnosed due to a small chest size and tracheobronchial hypoplasia. Furthermore, SOX9 mutations causing campomelic dysplasia have been related with 46, XY, sex reversal, with some variability in the degree of gonadal dysgenesis.

The malformations and syndromes associated with the BMP pathway include malformations in BMP4, which lead to microphthalmia syndromic 6 and orofacial cleft 11.2 BMP4 is a regulatory molecule that is involved with development in mesoderm induction, tooth development, limb formation, bone induction, and fracture repair. BMP4 is part of the BMP family and TGF-beta-1. When BMP4 is overactive, it causes microphthalmia syndromic 6 and orofacial cleft 11. 2 Microphthalmia syndromic 6 leads to hypoplastic kidneys, asbsence of optic nerves, underdeveloped genitalia, and brain anomalies such as a small cerebellum. Orofacial cleft is an opening or split in the roof of the mouth. Additionally, when BMPR2, which is bone morphogenetic protein receptor II, is mutated, it leads to pulmonary hypertension and pulmonary venoocclusive disease 1. The primary pulmonary hypertension is due to a heterozygous mutation that results in termination, frameshift, and nonconservative missense changes in amino acid sequence. 2 The pulmonary venoocclusive disease is to due a heterozygous transversion in exon 2 of the bmpr2 gene, which leads to a tyr40-to-ter substitution. 2 Venoocclusive disease is when blood flow is blocked in very small blood vessels in the liver, and hypertension is high blood pressure.

References:

1. http://omim.org/entry/608160?search=sox9%20&highlight=sox9

2. https://www.omim.org/entry/607932

Treating Pancreatic Cancer

Submitted by jgirgis on Fri, 04/28/2017 - 09:51

Pancreatic Ductal Adenocarcinoma (PDAC) is the third leading cause of cancer-related death in the United States.  In fact, only 8% of patients diagnosed with PDAC survive for more than five years from the point of their diagnosis (Indolfi, 2016). Though significant advances have been made in treating PDAC, patients diagnosed still generally have one of the lowest survival rates. This is due to its asymptomatic nature in early stages, meaning that it often goes undetected until the solid tumor has metastasized. Even when pancreatic cancer is detected in its early stages and has the potential to be resected via pancreaticoduodenectomy, most patients will develop metastatic disease. Knowing this, it is important that research surrounding the treatment of PDAC properly accounts for the nuances associated with a metastatic cancer and how it may differ from common therapies associated with a solid tumor.

Global Climate Change continued

Submitted by kmichaud on Fri, 04/28/2017 - 09:37

These rises in greenhouse gases are a combination of anthropogenic factors and naturally occurring processes, but have been significantly exacerbated by recent (within 200 years) anthropogenic emissions. Increased concentrations of CO2 and CH4 in the air are a product of agricultural and industrial production of CH4 (dairy farming) and from burning fossil fuels. The burning of fossil fuels in the form of coal or natural gas (CH4) results in an increase in CO2 and CH4 greenhouse gas concentration through the oxidation of organic carbon. As industrial practices increased over the past two centuries, burning of coal consistently increased global CO2 concentrations more drastically than background natural increases. 

Global Climate Change

Submitted by kmichaud on Fri, 04/28/2017 - 02:43

The causes of global climate change through significant overall warming has been a topic of significant debate politically. Among the scientific community, it is widely accepted that the recent rapid increase in atmospheric CO2 emissions and other greenhouse gases is directly a result of anthropogenic causes. As greenhouse gases, CO2, CH4 and N2O are capable of absorbing infrared radiation which is radiated into space from the Earth’s surface. These gases do not absorb visible light, allowing visible light to reach Earth’s surface and be absorbed as heat energy. This energy is then reflected as infrared radiation which is captured by the absorbing atmospheric gases, resulting in a warming effect. Overall warming is in an unfortunate, positive feedback loop with melting polar icecaps as frozen areas have higher albedo and can reflect more light. As the climate warms, icecaps will continue to decrease, resulting in more absorption of heat energy by land masses and increasing global temperatures. 

Turtle Shell Morphology

Submitted by kmichaud on Fri, 04/28/2017 - 00:12

Turtle shell morphology is an important determinant of how successful a species will be in its environment. Fully aquatic turtles, such as loggerhead sea turtles, have tear-drop shaped shells to increase their hydrodynamics during swimming. The first third of the shell should be the thickest point followed by significant tapering towards the posterior end of the animal to reduce the effects of drag. Though these species are well adapted to life in marine ecosystems, their heavy shells, flipper front limbs, and front-heavy carapace leave them significantly exposed on land. This is especially evident when females travel on land to deposit their eggs. Their movement is quite laborious, demonstrating how infrequently they make the journey.

Conversely, terrestrial turtles experience a selective pressure towards more domed carapaces. Domed shells provide more protection against predators by distributing bite forces around the shell, reducing the likelihood of breakage. This is especially evident in fully terrestrial tortoises. Semi-aquatic species such as mud turtles experience intermediate shell thicknesses to allow for protection again land predators while still facilitating efficient swimming. 

Role of Alx and Evolution

Submitted by jgirgis on Thu, 04/27/2017 - 23:44

            In the study titled, “Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton” by Hiroyuki Koga, the alx1 gene was proven to be necessary for the acquisition of the larval skeleton and played a necessary role in the evolution of the larval skeleton (Koga, 2016).

            In the study, echinoderm larvae were the model organisms used to see if alx1 is the gene that is necessary for the attainment of the larval skeleton. There are five classes of echinoderm, which include sea urchins, sea cucumbers, brittle stars, starfish, and sea lilies (Koga, 2016). The transcription factors, Ets1/2, Alx1, and Tbr, control the differentiation of primary mesenchyme cells that form the larval skeleton. Scientists pinpointed Alx1 to see if this gene was important with the evolution of the larval skeleton by inducing the expression of alx1 in starfish that do not have a skeleton.

            To induce the expression of alx1 in starfish, Koga and his team inserted mRNA that coded for Alx1 into the eggs of the starfish (Koga, 2016). This was done by utilizing microinjection. The goal was to increase the cell numbers of skeletogenic cells, and green fluorescent protein was inserted into starfish embryos, specifically the nuclei. Researchers measured the effects of inserting different types of mRNA. When the researchers inserted high levels of mRNA resulted in prevention of gastrulation (Koga, 2016). This then led to a halt in the process of development. Low levels of mRNA led to a high production of skeletogenic cells in sea urchin. But in starfish embryos, this did not occur (Koga, 2016).

            Koga’s team demonstrated that alx1 was necessary for the larval skeletons of sea urchins and sea cucumbers (Koga, 2016). However, alx1 was not expressed in starfish embryos, but was rather highly expressed in adult skeletogenesis. Koga and his team concluded that their data did not support the previous claimed statement that there is high expression of alx1 in embryonic and early larval stage of the starfish. There team also found that alx is replicated in the echinoderm lineage (Koga, 2016). Specifically, this study proved that in echinoderms, the expression of alx1 occurs more frequently in skeletogenic cells of adult and larvae. Starfish do not have tube foot spicules and in starfish, alx1 is expressed in the tube foot. Therefore, Koga and his team concluded that alx organically was necessary for coelomic development (Koga, 2016). One repeated paralog was involved with skletogenesis and researchers therefore concluded that alx is involved with the creation of the larval skeleton and the calcareous skeleton (Koga, 2016).

References:

1. Koga, Hiroyuki, Haruka Fujitani, Yoshiaki Morino, Norio Miyamoto, Jun Tsuchimoto, Tomoko F. Shibata, Masafumi Nozawa, Shuji Shigenobu, Atsushi Ogura, Kazunori Tachibana, Masato Kiyomoto, Shonan Amemiya, and Hiroshi Wada. "Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton." PLoS ONE. Public Library of Science, 11 Feb. 2016. Web. 24 Apr. 2017.

And even more repair

Submitted by sjurgilewicz on Thu, 04/27/2017 - 22:39

To fix depurination and deamination, base excision repair is used. In BER, glylocalyse flips out the wrong base and cuts it off. It is called apurinic or apyrimidinic once the base has been cut out. Next, AP endonuclease cuts the sugar and the phosphate out. DNA polymerase and ligase put in the new nucleotide and seal the gap. Thymine dimers, which are covalently linked and distort the helix, are created by UV radiation. This is a bulky distortion in the DNA and DNA polymerase cannot make it through. Some special DNA polymerases can replicate using this damaged DNA, but they are error prone and not used often. Thymine dimers are fixed by nucleotide excision repair. In NER, the nuclease cleaves around the bulky lesion. Helicase is required to pull apart the DNA, but it is a specialized helicase. Clamps are needed for BER & NER to recruit proteins and active the excision.

Xeroderma Pigmentosum is a rare recessive disorder, where UV damage cannot be repaired in the DNA through NER. Skin lesions and skin cancer occur from the sun.

Double strand breaks in the DNA result in cancer, premature again, apoptosis and chromosome reengagement. The cell does do breakage on purpose during recombination and VDJ. To fix accidental breakage, non-homologous end joining and homologous rearrangement are used. Non-homologous ending joining happens by nucleases come in and create blunt ends and remove several bases and seals back together. Loss of genetic information occurs but it is very commonly used in cells during G1. Homologous rearrangement requires for a separate piece of DNA that the matches the broken on exactly. The DNA is completely repaired. The 3’ end overhangs and invades the other strand that looks like the damaged DNA and base pairs. DNA polymerase synthesized across the area using the other strand as template. Ligase fixes the nick. This repair occurs in s phase, g2 phase, m phase. Basically when another copy of the DNA is present. 

Pages

Subscribe to Writing in Biology RSS