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Sturgeon PP

Submitted by klaflamme on Fri, 05/03/2019 - 11:16

The Conte Research Center is addressing how the sturgeons are being affected by waste in the area they live. This is an observational study where they take sturgeons from the area and run chemical tests on them. They have found that their endocrine systems have been affected negatively as it has affected sexual development. Males have been found to have more female qualities as a result. Endocrine disruptors could be affecting the newly born sturgeon. To address this, the gametes must be analyzed for any abnormalities and differences between sturgeon with these problems and sturgeons without from birth must be analyzed.

JasmonicAcid Discussion

Submitted by klaflamme on Fri, 05/03/2019 - 11:03

As treatment with jasmonic acid was predicted to negatively growth, our results of root and shoot biomass supported this hypothesis. Our results of inhibited growth are consistent with previous studies show jasmonic acid as a growth inhibitor to plants (Dathe et al. 1981; Redman et al. 2001; Koussevitzky et al. 2004). Root weight for treated plants were significantly lower than root weight for control plants. Previous literature shows that root growth of plants treated with jasmonic acid should be significantly effected (Yu et al. 2000; Tung et al. 1996). However, it has been shown that jasmonic acid deters herbivores from consuming the roots of the plant (Lu et al.). Although root mass was significantly affected by treatment, the roots of these plants may be less preferable to herbivores. This is something that would require further experimentation.

Experimental design PP

Submitted by cnwokemodoih on Fri, 05/03/2019 - 09:14

In an effort to extend the expression data in Phytozome, we designed an experiment to study Bradi3g27407 gene expression under 5% glucose growth conditions. To explore this, we conducted an experiment to study expression levels in root samples in the presence and absence of 5% glucose. We chose root samples because that is where our gene is most expressed, as indicated by our results from the e-FP browser. We used 8 root samples (5cm, young) from Brachypodium distachyon plants, growing 4 experimental samples in MS medium plates containing 5% glucose and another 4 control samples in MS medium plates without 5% glucose. We grew the plants at optimum temperature and light conditions: 24℃ day, 18 ℃ night. We created primers for the reverse transcription reaction, using primer3 software, so that they flanked introns but bound to exon sequences. The forward primer was 5’-tacaaggggaagatcagggc-3’ and the reverse primer was 5’-ccgcttgatctccttctcca-3’. These were so that the length of the sequence between the primers (not including the intron sequence) was 321bp (Figure S3). In Figure S3, the texts highlighted in yellow are the exon sequences, that highlighted in green is the intron sequence and the texts with red font color are the primers.

Human Evolutionary Genomics

Submitted by sfairfield on Fri, 05/03/2019 - 06:47

        DNA evidence has dramatically expanded our knowledge of the human evolutionary tree. Since the discovery that genetic material could be recovered from ancient organisms in 1984 (Higuchi et al. 1984), the study of ancient DNA (aDNA) has advanced rapidly. Certain factors can complicate the collection and analysis of aDNA, such as advanced age, the surrounding environment, and the collection technique, which can lead to degradation via cross-linking, deamination of cytosine, and fragmentation, as well as contamination due to extraneous microbial DNA and exposure to modern human DNA during extraction. Despite these difficulties, the revelation that archaic DNA can be sequenced, in conjunction with the sequencing of the human genome less than twenty years later (2001), provided the foundation from which the field of human evolutionary genomics arose. The insights gained about humans closest extinct relatives, Neanderthals and Denisovans, has been particularly impactful. These archaic human populations branched off from the modern lineage early in the Middle Pleistocene, approximately 750,000 years ago, and then separated from each other around 390,000 years ago. Many modern humans carry DNA derived from these archaic populations due to interbreeding during the Late Pleistocene, a period spanning 126,000 to 12,000 years ago (Slon et al. 2018).  In just the last decade, genomes have been recovered from Neanderthals and Denisovans. This has resulted in the determination that Neanderthals account for between 1% and 4% of the ancestry of people outside sub-Saharan Africa (Green et al. 2010), and Denisovans contribute from 1% to 6% of the ancestry of people in island Southeast Asia and Oceania (Meyer et al. 2012). These genomes provide information about the phenotypes of archaic peoples, insight into interactions between them and modern humans, and evidence of their contribution to the biology of modern humans. 

Epigenetic Effects in Monozygotic Twins

Submitted by scasimir on Thu, 05/02/2019 - 23:35

Monozygotic (identical) twins develop from a single egg fertilized by a single sperm that divides and gives rise to two zygotes. Thus, monozygotic twins are genetically identical, in the sense that they possess identical DNA sequences, but they often differ somewhat in appearance, health, and behavior. The nature of these differences in the phenotypes of identical twins is not well understood, but recent evidence suggests that at least some of these differences may be due to epigenetic changes. In one study, Mario Fraga, at the Spanish National Cancer Center, and his colleagues examined 80 pairs of identical twins and compared the degree and location of their DNA methylation and histone acetylation. They found that DNA methylation and histone acetylation in identical twin pairs were similar early in life, but that older twin pairs had remarkable differences in their overall content and distribution of DNA methylation and histone acetylation. Furthermore, these differences affected gene expression in the twins. This research suggests that identical twins do differ epigenetically and that phenotypic differences between them may be caused by differential gene expression.

Sensory Processing Signal Transduction Mechanisms

Submitted by ewinter on Thu, 05/02/2019 - 23:29

Signal transduction, in a sensory processing sense, is the conversion of energy into a neural signal. It occurs in receptor cells located in sensory organs such as the ears, eyes, and hands. Receptor cells are responsive to certain types of energy, but not others. In the cochlea (inner ear) hair cells located in the basilar membrane have stereocilia, which are hair-like structures that touch the tectorial membrane. Sound vibration causes hair displacement and opens mechanically gated ion channels, which causes the cells to depolarize and release neurotransmitters. These cells do not fire action potentials. There are four different types of touch receptors: pain, touch, vibration, and stretch. These can be found subcutaneously all around the body. Each touch receptor type has a distinct pathway to the brain. The visual system detects both brightness and contrast. Photoreceptors perform signal transduction. There are two types of photoreceptors: scotopic (rods), which work in dim light, and photopic (cones), which govern vision of colors. The visual pathway crosses sides at the optic chiasm, so the right visual field is processed in the left occipital lobe, and vice versa.

Orgo lab results PP

Submitted by jhussaini on Thu, 05/02/2019 - 19:14

Trimyristin was isolated from nutmeg through the processes of micro-scale filtration and recrystallization, and was then reacted to produce myristic acid. The trimyristin was recrystallized twice to collect it in the highest purity. The percent yield of the second recrystallization (83.29%) is higher than percent yield of the first recrystallization (71.88%). The higher percent yield shows that a greater proportion of impurities were removed after the second recrystallization. The melting points of the trimyristin after the first and second recrystallizations also indicate the difference in purity between them. The melting point of trimyristin after the first recrystallization is 52-55 ºC, which is lower than its theoretical melting point of 56-57 ºC. A lower melting point indicates that there are more impurities in the compound. In contrast, the melting point of the trimyristin after the second recrystallization is 56-57 ºC. This value matches the theoretical melting point of trimyristin and it is higher than the previous melting point, both of which indicate its high purity. The melting point of the trimyristin that was twice recrystallized also has a narrower melting point range of 1 ºC, which demonstrates the homogeneity and purity of the substance. The melting point of myristic acid was observed at 53-54 ºC. The purity of the myristic acid is shown by the narrow melting point range. The theoretical melting point of myristic acid is 54.4 ºC. The myristic acid formed in this experiment is pure because it is close to this value.

Phylogenies Perfect Paragraph

Submitted by sditelberg on Thu, 05/02/2019 - 13:05

With regard to the carnivorans, the character "tail" has two states. In this phylogenetic analysis, an elongated tail is the ancestral character state (scored with a 0) and a short tail is the derived character state (scored with a 1). In phylogeny A, a short tail is hypothesized to have evolved after the split between otters and the taxa of bears, sea lions, walrus, and seals. This relationship proposes that a short tail is the synapomorphy for the monophyletic group of bears, sea lions, walrus, and seals. In phylogeny B, a short tail is hypothesized to have evolved twice, exhibiting homoplasy. A short tail here is a derived trait for the seals, but it is also a shared derived trait for bears, sea lions, and walrus. However, there are a few separate divergences between seals and this group, and the common ancestor is hypothesized to have an elongated tail. In phylogeny C, a short tail is hypothesized to have evolved twice as well, but then was lost in one lineage branch. A short tail is a derived trait for the bears, but it also initially evolved as a shared derived trait for taxa of sea lions, walrus, seals, civets, hyenas, and cats. Cats, hyenas, and civets then lost this short tail, demonstrating an evolutionary reversal. In phylogeny D, a short tail evolved once in the lineage to include the monophyletic group branching from seals to dogs, but it was lost later in the taxa of otters, raccoons, and dogs, exhibiting another evolutionary reversal. Based on this trait and the parsimony principle, phylogeny A is the most likely evolutionary hypothesis as the tail trait only evolved once in the lineage and was not subsequently lost. The parsimony principle guides us to the evolutionary tree with the fewest character-state changes, which is usually regarded as the best.

Neanderthal/Human hybrids

Submitted by sfairfield on Sat, 04/27/2019 - 18:18

            Neanderthals are thought to have disappeared approximately 39,000–41,000 years ago, but due to overlapping chronologically and geographically with modern humans' ancestors, they contributed 1–3% of the DNA of present-day people in Eurasia. In the study by Fu et al., DNA from a 37,000–42,000-year-old modern human from Peştera cu Oase, Romania was analyzed. Although the specimen contained small amounts of human DNA, an enrichment technique was used to isolate genomic sites that were distinct between Neanderthals and present-day humans. They found that  6–9% of the genome of the Oase individual was derived from Neanderthals, more than any other modern human specimen sequenced to date. Three of the chromosomal segments of Neanderthal ancestry were measured to be over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual did not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.


Week13 PP

Submitted by mqpham on Sat, 04/27/2019 - 13:33

Evolutionary development is a branch of biological study. Two lines of research in the field have developed across a span of twenty years since its conception. One branch of evolutionary development focuses on discrete and qualitative changes in phenotype. The other focuses on research done through investigating complex phenotypes though quantitative developmental phenomena. However, there is potential for the two to be used together in explaining processes and mechanisms of evolutionary development over time. In recent years, evolutionary development offers insight on specific molecular connections between genotype and morphology. Still, the importance of how the morphology interacts with the environment will make the final determination on the fitness of the genotype. Therefore, evolutionary development has a greater potential if it is broadened from the fine details of the genotype all the way to how those genotypes affect resource use (Irschick, Albertson et al, 2013).


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