Blogs

The diversity of colunteer species will be recorded by counting the number of different species present. Pictures will be taken and each volunteer species will be identified. Pictures will be labed as figures and will be recorded in the figure section; the different volunteer species will be recoded in a Google spreadsheet. The height of the volunteer species will be measured from the soil to the tallest point of the volunteer species. The length of the volunteer plants leaves will be measured. If there are multiple of the same species, the average of the lengths of leaves will be measured. If there are multiple of the same species, the average of the lengths of leaves will be calculated and recorded. If there are more than 10 leaves of the same species, the average of 5 leaves wiill be taken. The total area of the individual pot and 4x4 meter plot that is covered by volunteer plants will be recorded. The number of leaves per stem of the volunteer plant will be counted and recorded. If there are volunteer plants with multiple stems, the average number of leaves per stem will be taken. The height of the host will be measured. Alll measured data will be recorded in centimeters.

The article “Four new DNA letters double life’s alphabet,” describes how synthetic bases are used to form a DNA structure. The ability to generate synthetic DNA that even slightly resembles how biological DNA functions is truly phenomenal. However, from a standpoint that defines life in terms of purpose and function, if the synthetic bases are unable to give rise to the molecules necessary for survival or unable to replicate, then I would consider the DNA as non-living. Even if the DNA looks similar in structure and shares a few of the functions of biological DNA, it would be unable to preserve its identity. This demonstrates my initial point that even if something shares some characteristics with a living thing, that does not make it alive.

The article “Four new DNA letters double life’s alphabet,” describes how synthetic bases are used to form a DNA structure. The ability to generate synthetic DNA that even slightly resembles how biological DNA functions is truly phenomenal. However, from a standpoint that defines life in terms of purpose and function, if the synthetic bases are unable to give rise to the molecules necessary for survival or unable to replicate, then I would consider the DNA as non-living. Even if the DNA looks similar in structure and shares a few of the functions of biological DNA, it would be unable to preserve its identity. This demonstrates my initial point that even if something shares some characteristics with a living thing, that does not make it alive.

The warming climate has a known bleaching effect on coral reefs. This paper highlights the significant effects of the climate on coral bleaching at deep, mesophotic depths. These bleaching results demonstrate the limitation of deep coral reefs as thermal refuges as the climate continues to warm. The study collected data on the temperature and severity of bleaching at different sites along the Great Barrier Reef and the Western Coral. In 2016, a mass bleaching event in this area caused the death of 30% of shallow-water corals. Results showed more severe bleaching for shallow-water corals in relation to deep corals. Although the severity of bleaching was significantly less for deep corals, the impact is still substantial and is predicted to worsen in the future. This result is devastating because bleaching effects are not only harmful to the coral, but also to all of the millions of animals that depend on the reefs for survival. 

This paper focuses on how interstitial annelids evolved to live in interstitial spaces. Three hypotheses on how this evolution occurred include progenesis, miniaturization, and that the interstitial space was originally an ancestral home to Bilateria. Progenesis is the retention of juvenile characteristics in the adult form, and miniaturization is the evolution of a small body size. Progenesis is the commonly accepted hypothesis for interstitial annelid evolution, though it has not been fully explored, which is a reason this study was conducted. The authors of the study applied a phylogenomic approach by generating transcriptome sequencing data. They found relationships and similarities between clades to figure out how different annelids evolved in interstitial spaces. Progenetic evolution was found in Orbiniida, Eunicida, and Hesionidae. Evolution through miniaturization was found in Protodriliformia, Pisionidae, and other interstitial species. One of the conclusions they found was that the simple body organization and interstitial habitat of annelids are not ancestral traits of annelida. This result led them to reject the “Archiannelida” hypothesis. The authors also found that progenesis and miniaturization were equal in terms of significance as factors that caused annelids to evolve in interstitial spaces.

In contrast to snakes, anoles (a type of lizard) possess more limb structures such as the tibia and fibula. The presence of more limb structures is partially due to different expression patterns of the Sonic Hedgehog gene. A team of researchers (led by Leal and Cohn) found that in anole leg buds, expression is more sustained and in pythons’ expression is transient. The ZRS domain in anoles was also found to bind more strongly to transcription factors than the python’s ZRS domain. The differences between enhancer elements for the Sonic Hedgehog gene indicate how the gene was able to evolve over time. Mutations that have lowered enhancer binding could have down-regulated the Sonic Hedgehog pathway, leading to limb reduction in snakes. In many vertebrates from anoles to humans, the amount of limb development shows a direct relationship with the activity of the Sonic Hedgehog enhancer. 

The Hedgehog signaling pathway plays a role in the loss of limbs in snakes. According to the fossil record, ancestral snakes had limbs, which became reduced over the course of evolution. Some species of snakes such as boas and pythons still have a rudimentary femur and claw, while in other species such as cobras, limbs have disappeared completely. This phenotypic difference suggests that limbs were lost over time. The Sonic Hedgehog gene is regulated by a limb-specific enhancer called the zone of polarizing activity regulatory sequence (ZRS). This enhancer is conserved in all invertebrates and accounts for differences in limb development in vertebrates. A team of researchers led by a genomicist named Visel found that by substituting the ZRS of mice with the ZRS of snakes caused truncated limbs. In contrast, substituting mice with human and fish enhancers caused legs to grow normally. Sequence analysis of the ZRS in snakes showed deletions, which resulted in weak expression of Sonic Hedgehog and truncated limbs. The varying degrees of expression of Sonic Hedgehog is a possible cause of limb reduction in snakes.

We will use the drug J113863, a CCR1/3 receptor antagonist. Mitra and colleagues showed that this drug successfully blocked the homing of ovarian cancer cells to normal omental fibroblasts transfected with anti-miR-214 and anti-miR-31- an induced CAF phenotype. We will deliver this on the biopolymer sheet. The biopolymer sheet will be put directly on the omentum during surgery. This delivery method will allow introduction of the drug directly on its target - the omental fibroblasts and any metastatic cancer cells. CCL5 will be unable to bind to its receptor and therefore the receptor will not transduce the signal to the NF-kB signaling pathway, which therefore will inhibit the epithelial to mesenchymal transition of ovarian cancer cells.  

Metabolic pathways are connected indirectly so that energy released by catabolic pathways is transferred to anabolic pathways. There are two main forms of transfer, and one of them is electrons. Oxidation-reduction, or redox, reactions transfer electrons between molecules. To be oxidized means to lose electrons, and to be reduced means to gain electrons. For every oxidation, there must be a reduction since there are no free electrons in cells. In order to distinguish which molecules will be reduced while another is oxidized, the reduction potential is determined. The reduction potential is the affinity for electrons, or the likelihood of being reduced. It is determined experimentally by comparing the molecule’s reactivity to hydrogen under standard conditions. If its oxidized form has a higher affinity for electrons than hydrogen, it accepts electrons and becomes reduced. On the other hand, if its oxidized form has a lower affinity than hydrogen, its reduced form donates electrons and becomes oxidized. The reduction potential is measured in volts, and a positive potential indicates spontaneity. There is an equation developed that relates the reduction potential to change in free energy, and the presence of a negative sign on one side indicates that a positive reduction potential means a negative change in free energy. This is parallel with the fact that a positive reduction potential means a spontaneous reaction.

The sonic hedgehog pathway is a third highly conserved pathway involved in tissue growth and repair as well as PaCSC self-renewal. In pancreatic adenocarcinoma, KRAS promotes sonic hedgehog expression via the inflammatory transcription factor NF-kB (Gu et al. 2016). The sonic hedgehog protein inhibits the receptor patched, which releases its inhibition of the protein smoothened. Smoothened leads to the activation and nuclear localization of GLI transcription factors, which regulates expression of target genes. An appealing target for this pathway is smoothened, and inhibitors BMS-833923 and PF-0444913 serve as effective treatments for pancreatic adenocarcinoma (Jia et al. 2019). These two inhibitors work most efficiently in combination with gemcitabine, but also have shown beneficial effects on their own (Jia et al. 2019). The researchers plan to incorporate these two smoothened inhibitors, BMS-833923 and PF-0444913, into their treatment as well to block the self-renewal of PaCSCs.