Drafts

The paper on song sparrows studies the effect of the environment on the trill song of chipping sparrows, with a focus on divergent solutions to signal deterioration as a result of intraspecific song variation. First and foremost, sounds propagate through the air as waves composed of rarefaction and compaction zones. The density of air particles in the compaction zones is measured as the sound’s amplitude, and the distance between compaction zones is measured as the sound’s frequency. Sounds suffer from two kinds of degradation: frequency -dependent attenuation and reverberation. Attenuation is defined as a decrease in sound intensity with increasing distance. Ideally, sound spreads spherically from the source and intensity decreases in proportion to 1r2, where r is the radius of the sphere. However, environments tend to be heterogeneous, and habitat as well as weather conditions cause excess attenuation on top of the attenuation predicted by spherical spreading. In addition to attenuation, reverberation contributes strongly to impeding signal transmission. As sound waves impact objects they are reflected, which can lead to scattering, slurring of syllable form, and often makes it difficult to distinguish successive elements. These effects are most pronounced in signals of high frequency, high bandwidth, high duration, and low internote time. In order to compensate for attenuation and reverberation in highly obstructed environments such as forests, birds often decrease the minimum frequency and the number of amplitude and frequency modulations of their signals. This type of environmental tuning has been found within single species’ subpopulations living in environments with different levels of obstruction. Therefore, since signals are the primary means by which songbirds compete with one another, for individuals to be able to compete with one other, they must make their signals heard. Commonly, in order to transmit their signals above background noise, birds tend to both increase the amplitude of their vocalisations - known as the Lombard effect - and to sing higher pitched songs. Lastly, amplitude and frequency modulated trills are often used by songbird females as measures of vocal performance, based on how close the male sings to the biophysical limit of the bandwidth to rate ratio. Females prefer males which sing closer to the biophysical limit of trilling and males with stronger trills are better at holding their territories. In urban environments with highly reflective structures and high background noise, trills suffer heavily from the effects of reverberation and therefore vocal performance is perceived as being poorer. In turn, this has an effect on how well males can both attract females and defend their territories, which could mean that urban environments could generate unique intra- and intersexual selection pressures. 

So why is this disease one of the most devastating ones and what does it look like on a neurobiological level? From a broader perspective, our brain only looks like a grey mush that may not be containing much. However, on a microscopic level, the sheer detail of how much goes on in there can be overwhelming. However, to make it simple, we will look at AD through two perspectives. Tau is a protein that in normal terms is actually there to be helpful. Our brain has microtubules that is necessary for transporting nutrients around the brain. The tau protein stabilizes those microtubules. However, by random mutation, this incredibly essential protein becomes a problem. It starts to entangle in parts of the brain that are responsible for memory, like the hippocampus. With the lack of nutrients, the neurons (nerve cells) in the brain start to die. Another vital player in AD is beta-amyloid. Beta-amyloid is the product of the precursor amyloid protein. Usually, the fluid in our brain (CSF) is able to wash out the amyloid build up. However, when it starts building up as plaques it can get to a toxic level, thereby causing cell death in the brain. With all this shrinkage, especially in the areas responsible for forming connections and making memory, it becomes increasingly difficult for people to remember details about their lives. 

The first deviation from procedures happens during the MC1R sequencing preparations. After so many PCR reactions, it is not surprising that some groups would lose their test tubes as the heat from the thermocycler erases the labels on tubes. Unfortunately, we were confident that our tubes were gone. Despite remembering the color of our labels as well as where we placed them, none of the tubes from both genetic lab sections matched our description. Loss of the MC1R PCR products resulted in us having to use Dog 5’s MC1R sequencing, which came out as below average, yet useable, quality.

In the comparison between Tasha the Boxer versus our sample dog, EMBOSS Needle showed many gaps between the reference sequence and our sequence. The gaps could be due to the poor quality that came up from the files. MC1R PCR products may not have been amplified to a great extent due to lack of dNTPs or primers. The SNP at nucleotide 790 helps conclude that our dog does not have a melanistic mask because our sequence does not have the same nucleotide (C) at 790 as the reference sequence (G). The SNP at nucleotide 808, 832, and 901 are specific to Siberian Husky dogs, which may suggest our dog is a Siberian Husky, or at least related to a breed of Siberian Husky. The relationship was no surprise because our first BLAST results showed that our MC1R sequence could be related to a Siberian Husky breed with 97.85% identity. MC1R files showed that at the MC1R gene is homozygous at nucleotide 916, which means the dog cannot be yellow because our dog must have two copies of nonfunctional MC1R (the e allele) to not produce eumelanin.

The religious violence then came not too long after, President Hosni Mubarak has urged Egypt's Muslims and Christians to stand united against terrorism after a bombing outside a church in Alexandria in 2011. At least 21 people were killed and 70 hurt in the suspected suicide attack, which happened during a New Year's Eve service at the al-Qiddissin Church. You may have thought this violence would reside but on 11 December 2016, a suicide bomber killed 29 people and injured 47 others at St. Peter and St. Paul's Church (commonly known as El-Botroseya Church). Another example being 2017, where bombs went off at two Coptic Christian churches in Egypt on April 9th, killing more than 40 people and injuring dozens of others. The attacks occurred on Palm Sunday ― one of the holiest days in the Christian calendar. ISIS claimed responsibility for the attacks, which were aimed at a vulnerable religious minority on one of the most important days on the Christian calendar

When I tell people, I am Egyptian, I get nothing but “Wow! That must be amazing!” or “Were you born in a Pyramid?” It is true that Egypt carries one of the 7 wonders of the world; The Great Pyramids of Giza. However, beneath the beauty of this country comes violence, a violence that saddens my heart and could potentially affect my family lineage. I am Coptic Orthodox. Currently, we occupy 6-8% of the Egyptian population. The city “Alexandria” is even named after the Alexandrian priest, Arius. It is sad to see that for me, as we were once the dominant religion in Egypt, before Islam took over. Currently, it is estimated that 94.9% of Egyptians are Muslim. Although both religions consist of many amazing individuals, problems occur when two religions have different beliefs but reside in the same country, and are a part of ISIS, a terrorist militant group.

For plants, animals and humans to live healthy lives, the soils must also be healthy. The determining factor for soil health is often soil organic matter. To better manage the soil and maintain a healthy ecosystem this data is used to develop agricultural practices. For this to work, input of soil organic matter needs to exceed output of soil organic matter. This data helps us identify which regions are more at risk to loss of soil organic matter and why. Water availability is also taken into consideration and both of these systems are looked at locally and globally. This map has units of measurements to rate these systems. Both global and continental scale factors (temperature, precipitation) are taken into account as well. This system does not take irrigation into account.

Hundreds of different cell types in the human body are formed during embryonic development. These fully formed cells are derived from just a few identical stem cells. Researchers from the Faculty of Medicine at the University of Freiburg have now deciphered a control mechanism in these stem cells that decide what kind of cells they turn into. They found that there are different genes for each cell type and the amount of gene expression for those genes in stem cells determine what kind of cells they will turn into. The results of the study are a crucial step in understanding the mechanisms of how stem cells develop into different types of cells during embryonic development. 

The dispersion of Emperors to the frontiers must have resulted in a significant shift in societal and cultural expectations. As revealed in Symmachus letter, Rome is in desperate need of financial assistance claiming "for some time now the provinces appointed for the purpose have contributed nothing of their usual revenues". Symmachus described how the people of Rome expect a certain lifestyle: "It is not greed that inspires the desires which the humanity of the age has aroused; rather, the precedents you have set are the source of our confident expectations". Symmachus flatters the emperors in this letter by making likely exaggerated claims that every Roman holds emperors in their hearts. He was likely trying to establish a connection between the emperors who prefer the frontiers to the people of Rome. If Symmachus was successfully able to establish this connection then he may have hoped the Emperors would send more aid. Symmachus seems to claim that the Romans were entitled to such riches because they were previously accustomed to it.

A new study done by researchers at Colombia University has identified serotonin as the chemical that triggers the body's startle response in fruit flies. This study shows that when a fruit fly is starlted with unexpected changes to its surroundings, levels of serotonin rise and this helps to stop the fly in its tracks. Since serotonin also exists in people, the results in this study may be a clue as to what happens inside our body with the serotinin levels when we become startled. Serotonin is closely associated with mood and emotion, but more recently, it has been shown to affect the speed of animals movement. The researchers found that serotonin levels in walking fruit flies varied when experiencing additional factors, such as different temperatures, walking upside down, and walking while hungry. Researchers found the biggest significant changes in serotonin levels when a sudden change to the fruit fly's environment occured, or when they were startled.

Plants have many ways of reproducing. Many plants sexually reproduce by pollination of eggs with pollen to create a diploid zygote from two gametes, much like how mammals reproduce. Some plants go into haploid spore forms that can live in a life cycle on their own by mitosis that then fuse together to form a diploid that creates spores again. And some plants, even with diploid genomics, reproduce by cloning. Such plants include strawberries, quaking aspen trees, poison ivy, and spider plants. Clonal growth has many advantages over other ways of reproducing. Firstly, cloning themselves allows for daughter plants to become fully formed by remaining connected to the parent plant, sharing nutrients, water, sugars, and other vital molecules until the daughter plants can be completely independent. Secondly, with quaking aspens as an example, there are plants that do not severe the connection between the parents and daughter plants, and instead maintain connections that allow the plants to share nutrients, signal molecules, and everything in them for as long as they live. This allowed quaking aspens to be the largest single organism in the world, covering hundreds of acres and living as long as four thousand years- having thought to started growing after the most recent ice age.