Writing in Biology - Section 1

Data was collected on November 19th, 2019 in the Biology lab at Umass Amherst in Amherst, MA. The subject of study was ,Gryllus spp., the common field cricket found in the Northeast. The goal of this data collection was to measure the frequency at which male Gryllus spp. exhibited courting activities or competitive behaviors while in the presence of another male, and a female. Thirty crickets were used for this experiment, 20 males and 10 females. Before the experiment began, the crickets were identified as either male or female, and placed in two separate containers by the observers based on sex.

One important use of electrocommunication in weakly electric fish species is conspecific and heterospecific recognition. The use of electric signals for this purpose has been demonstrated in both wave-type and pulse-type fish (Fugère & Krahe 2010, 213; Dunlap et al. 2010, 213; Worm et al. 2018, 1). Counterintuitively, some weakly electric fish preferentially avoid conspecific signals, and this has been attributed to differences in their jamming avoidance response (JAR) (Stamper et al. 2010, 368). Interestingly, it has been hypothesized that JAR doesn’t just serve to avoid interference among fish living in a group, but also as a means of intragroup communication (Stamper et al. 2010, 376; Petzold et al. 2018, 1). 

Species recognition has been demonstrated in the wave-type brown ghost knifefish, Apteronotus leptorhynchus (Fugère & Krahe 2010, 213; Dunlap et al. 2010, 2234). Like other wave-type fish, A. leptorhynchus modulates the frequency and amplitude of its EOD, to produce communication signals generally referred to as “chirps”, “rises”, and “interruptions” (Fugère & Krahe 2010, 213). It has been shown that the waveform of the electrical stimuli A. leptorhynchus encounters does not affect its chirping or approach behaviour whereas frequency changes have a strong effect on chirping and approach behaviour (Fugère & Krahe 2010, 231). This has been corroborated by another study, whose findings show that A. leptorhynchus chirp rate changes when the fish is presented with electrical stimuli that have different frequencies (Dunlap et al. 2010, 2234). Thus, current findings suggest that A. leptorhynchus uses changes in frequency and not waveform to recognise conspecifics (Fugère & Krahe 2010, 234). It has also been shown that A. leptorhynchus can distinguish between conspecifics and heterospecifics, chirping at higher rates in response to conspecifics and at lower rates in response to heterospecifics (Dunlap et al. 2010, 2241). However, there lacks research into whether or not heterospecific type chirp response has any communicative value in A. leptorhynchus (Dunlap et al. 2010, 2241). In addition, the evolutionary origins and adaptive value of this type of electrocommunication in A. leptorhynchus have yet to be discovered.

Only relatively recently, it was shown that a pulse-type fish, Mormyrus rume proboscirostris (M. rume), also uses electrical signaling for species recognition (Worm et al. 2018, 1). In the absence of both vision and the lateral line system, M. rume can rely solely on its electrocommunication system to track and match a source of conspecific electrical signals (Worm et al. 2018, 1). M. rume recognise each other via stereotyped inter-discharge intervals (IDIs) that consist of a short sequence of double-pulses, synchronized at approximately the same frequency as the conspecific signal they receive (Worm et al. 2018, 4). Additionally, and as opposed to A. leptorhynchus behaviour, it was shown that M. rume uses conspecific electrical signals to orient itself spatially, as observed by its following behaviour when presented with a moving source of conspecific signals (Worm et al. 2018, 10).

Carbon sequestering is the process of removing CO2 from the atmosphere and oceans and allocating it to long-term storages called reservoirs. Photosynthesis of ocean aquatic plants drives the oceanic biological CO2 pump, where CO2 from the atmosphere enters the ocean from the atmosphere. Greater than one-third of human-produced CO2 ends up in the ocean where it is introduced to the aquatic photosynthetic cycle. Locations with large collections of seaweed and algae act as carbon sinks, particularly in coastal regions where it is ideal for seaweed aquaculture. These coastal vegetation hot-spots represent less than 2% of the ocean surface, yet contribute close to half of the carbon burial in the coastal and global ocean however, more than 25% of the CO2 sink capacity of these ecosystems has been lost and the overall spread of these habitats is decreasing due to climate change and development.  These places are naturally proficient at carbon sequestering, so increase in seaweed farming on coastal regions would only increase the sequestering potential. Seaweeds are the most productive macrophytes, especially in relatively shallow, high light, coastal environments such as aquaculture farms. Their astounding ability to take in CO2 and convert it through photosynthesis results in forms of carbon which are far easier to sequester and break down, unlike the harmful buildup of carbonic acid. 

The TYRP1 gene in Canis Lupus Familiarus, known commonly as the domesticated dog species, has been well studied. Since the genes of dogs have been sequenced and thousands of alleles compared, it was revealed that this gene, TYRP1, contains a very common and highly conserved mutation. The wildtype DNA sequence for the gene contains a segment 5'-TGGGGGAA-3'. In the mutation the sequence is simply 5'-TGGAA-3'. This shows a three nucleotide deletion that removes a set of three Gs. The reason this mutation is able to be so conserved is because three nucleotides form one single codon, allowing for the deletion to not cause a frame shift in the gene so that only one single amino acid is missing and the remaining correct amino acids are conserved. This mutation causes a disfunctional protein that acts as an enzyme in melanocyte cells that produce colored pigment in the dog hairs. Without a functional TYRP1, a brown pigment cannot be transformed into a black pigment. Because this defect has no toxicity in the accumulation of the brown pigment, the mutation was never selected against and gained frequency in population, also thanks to breeding. 

The size of the digested bands must be looked at and referred to the paper by both Berryere et al.’s paper (2005) and Schmutz et al.’s paper (2002), to analyze the gels performed for Agouti and TYRP1. Counting down from the 500 bp band, we cannot see the 100 bp band. A reason for this is that it may have traveled too far down the gel for us to see it. The Agouti gel does not show bands below 200. Berryere et al. (2005) says that "After digestion with BsmA1 the ay-allele yields fragments of 42, 90, 153 bp; other alleles yield fragments of 42 and 243 bp.” Since our digested band yields a length of around 200-300, we can conclude we do not have the ay allele, but still may possess the a^w, a⁺, or a allele. The TYRP1 gel shows bands at 73 bp (visible) and 48 bp (not visible but assumed using paper) for MnIl, and bands of 93 bp (visible) and 28 bp (not visible but assumed using paper) for Acil. Schmutz et al. (2002) says that Acil digestion causes “animals with the premature stop codon cut to bands of 28 and 93 bp” while MnlI digestion causes “animals without the proline deletion cut to band sizes of 48 and 73 bp.” From this, we can conclude that our dog is mutant for the premature stop codon in exon five, and wildtype for the proline deletion in exon five. The study states that “all 43 of the brown group carried two or more of these sequence variants,” while “0 of 34 in the black group carried two or more of these variants” (Schmutz et al., 2002). If our dog has the third variant, we cannot confirm whether the dog will be black or brown from the TYRP1 analysis. However, the variant in exon two is rarely found, suggesting that our dog is more likely to be black in coat color. If we could select one more allele to analyze, we would analyze this third rare variant in exon two because it would conclude whether our dog is black or brown. Analysis of the third variant would be performed by seeing if there is “a serine substitution of a cysteine at amino acid 41 in exon 2” (Schmutz et al., 2002).

Copper hospital beds kill bacteria. A new study has found that copper hospital beds in the Intensive Care Unit (ICU) harbored an average of 95 percent fewer bacteria than conventional hospital beds, and maintained these low-risk levels throughout patients' stay in hospital. In the United States, hospital beds are the 8th leading cause of death. This is not okay! The hospital should be a safe place to go when someone is already sick, not a place to receive more bacterias and infections. They are among the most contaminated surfaces in medical settings.  This idea came from ancient Ayurveda, when drinking water was often stored in copper vessels to prevent illness. Additionally, copper has been previously studied to have antimicrobial properties. 

This idea is new and is still being studied. To conduct an experiment for this, you need a control group, and a experimental group. Ex: comparing plastic beds with copper beds. Nearly 90 percent of the bacterial samples taken from the tops of the plastic rails had concentrations of bacteria that exceed levels considered safeAlthough these are not yet on the market, and will be costly, this will be beneficial for the future of our healthcare industry and microbe control.

There is a relationship between the texture of the soil and hydraulic conductivity. That relationship revolves around matric potential. At saturated conditions, hydraulic conductivity is much higher than potentials that are in unsaturated conditions. When there is a high moisture content, the hydraulic conductivity is higher in the sand than in the clay. At low moisture contents hydraulic conductivity is higher in the clay rather than sand. This phenomena occurs because sand has many more macropores and this allows moisture to move readily through the soil. That is why the graph shows the sandy loam soil’s curve dropping faster than the clay. Saturated flow takes place near zero ksat. This can be seen on the graph just before the sandy loam’s line starts to curve downward. In unsaturated conditions, the sandy loam ksat decreases. For the clay soil, the ksat is high in unsaturated conditions. This most likely has to do with the many more small pores that clay has versus sandy loams with macropores.

One of the many ramifications of climate change that is coming to the forefront of the climate change debate is ocean acidification. For many years the primary concern with climate change's effect on the oceans has been the rising sea level that could potentially flood coastal cities and force millions of people to relocate. While this is something that should take focus, ocean acidification is something that is affecting the ocean wildlife, something humans rely a great deal on for food. Besides the food, the ocean also contains many ecosystems that if destroyed can have a chain reaction, destroying other ecosystems that will eventually negatively impact humans. As carbon levels in the atmosphere increase, carbon dioxide diffuses into the ocean. Carbon dioxide likes to react with calcium carbonate, the material used to make shells and coral reefs, to make carbonic acid. As more and more carbon dioxide gets into the ocean, the more carbonic acid is created, lowering the pH level of the ocean to a more acidic level. Organisms in the ocean require certain conditions to thrive, and as the pH gets lower organisms cannot thrive in such acidic conditions. This is evident in coral reefs, where a process called coral bleaching is occurring. The acidic water makes the coral expel the algae that usually lives in, and has an endosymbiotic relationship with the coral. The loss of the algae produces a sickly white color (hence "bleaching"). Ocean acidification is just one cause of coral bleaching. Humans must crack down immediately to save our planet.

Geraldine Seydoux talked about how embryos determine body axis. She used the C.elegans as the model organism. Newly fertilized cell has two pronuclei -maternal and paternal – that fuse to one nucleus and cell division ensues to create a ball of cells. At one point the cell becomes asymmetrical – the smaller cell always ends up on the side of the posterior side and bigger cell on anterior side. But this had to be proven and linked to the adult cell. This research is shown by John Sulston who traced cell lineage of C.elegans and found that posterior side ended up being represented by the smaller cell. To dig in deeper – Professor Seydoux showed the gonads of the C.elegans (hermaphrodites) – oocytes had the maternal pronucleus and the sperms had the paternal – sperm fertilized the oocyte and the smaller cell ended up being at the posterior side, so the hypotheses were 1) the sperm determined the posterior side 2) that the oocyte directed the axis determination. They tested the first hypothesis: sperm induces posterior? They changed the position of sperm entry and the result was that that the embryo polarity was reversed. How did this work? They looked at the molecules involved in the oocyte cytoplasm. Genetic screening of wild types and mutants with symmetric cells and cloning those cells allowed them to identify the protein and their genes. 

Weakly electric fish are a subset of electric fish species that typically generate electric discharges under one volt (University of Virginia, n.d.). Both weakly and strongly electric fish have an electric organ in their tail composed of electrocytes that they can excite to cause electrical organ discharges (EODs), which they sense via electroreceptors embedded in their skin (University of Virginia, n.d.). Through this mechanism, weakly electric fish can electrolocate and electrocommunicate (Worm et al. 2018, 221). During electrocommunication, weakly electric fish encode information in their electrical discharges to transmit to each other information about species, age, gender, identity, and motivation (Zakon & Smith 2009, 611). Weakly electric fish species fall into two types: pulse-type fish which produce short, intermittent pulses of electricity and wave-type fish wich generate continuous A.C. electricity (University of Virginia, n.d.). This review aims to cover the last decade’s research into social electrocommunication in weakly electric fishes including: species recognition, jamming avoidance response, dominance, competition, and sexual dimorphism. Although there has been much research into the electrocommunication behaviours of weakly electric fish, it has by and large been observational research focused on proximate questions. As such, there is a lack of research into important ultimate questions concerning electrocommunication. Ultimate avenues of inquiry in future research may provide insight into why electrocommunication first developed, and why weakly electric fish species are confined to the South American and African continents (Moller 1995, 583). Studying the evolutionary and adaptive aspects of electrocommunication might be a critical step in elucidating important evolutionary relationships in freshwater fishes.