semans's blog

Foraging has long been studied with the underlying assumption of optimal foraging theory, which states that a foraging animal will try to maximize its energy intake. Thus, foraging behaviour can be described using two simple models: the prey choice model, and the marginal value theorem. The prey choice model has three elements: caloric value of a prey item (E), handling time (h), and search time (S). Profitability is the rate of energy intake for a prey item: Eh. There are two canonical prey item types, prey type 1 and prey type 2, the former has the highest profitability and the latter has the lowest profitability such that: 

E₁/h₁>E2/h₂

Therefore, the only time a predator should eat prey type 2 is when:

E2/h₂>E1/(h₁+S₁)

This yields three predictions: the animal will always try to maximize caloric intake; the animal will instantly shift to the less profitable prey type once the inequality is met; and S2 will not affect the animal’s choice to eat prey type 2. The marginal value theorem is a description of the movement of an animal from one patch to the next. This is a graphical model that describes the optimal amount of time the animal will spend in a patch. The cumulative energy gain in a given patch will increase rapidly and then level off, the tangent to that curve from the point indicating the animal’s travel time gives an optimal point at which the animal should leave the patch to maximize caloric intake.

There are four primary methods used in biology to produce transgenic organisms: transgene engineering, knock-in engineering using embryonic stem (ES) cells, knock-in engineering using CRISPR, and viral gene delivery. Here, I will go over the first two of these methods. Transgene engineering was the first time foreign genetic material was incorporated into an animal’s genome. Palmiter and Brinster added the gene for human growth hormone (HGH) to zygotic cells during the stage at which the genomes of each parent cell are fusing in order to get random incorporation of the gene. In order to get expression of this gene they also packaged a promoter with the transgene which would ensure its expression in transformed mice. The next step in genetic engineering came with knock-in engineering in ES cells developed by Capecchi, Martin, and Smithies. This method involves using a new kind of transgene that lacks a promoter but has gained a neomycin resistance gene and homologous arms. A promoter is unnecessary as the arms of homology will target the transgene to a specific place in the genome after a promoter that is already active. The transgenes are then added to cultured ES cells. The cells that take up the transgene and undergo a double-stranded (DS) break that matches the transgene’s arms of homology get transformed. Then, the antibiotic neomycin is added to the cultured cells to select for the cells that were transformed. These transformed cells are injected into a blastocyst where they can be expressed.

The effects of temperature on insect activity have been researched across taxa ranging from Diptera (Bowler & Terblanche, 2008) through Coleoptera and Lepidoptera (Briere et al., 1999) to Hymenoptera (Abou-Shaara, 2014). Throughout these orders, insects demonstrate the ability to detect temperature, which can help them perform tasks from determining foraging window timing (Vicens & Bosch, 2000) to finding the warmest location in a stack of wheat (Flinn & Hagstrum, 1998). Understanding the factors that influence insect behaviour is critical to advances in sustainable agriculture practices and conservation management. In this study, we analysed the effect of environmental temperature on the foraging behaviour of the large milkweed bug (Oncopeltus fasciatus). In order to better preserve the Apocynaceae and Asclepiadaceae plant families (here collectively termed "milkweed") that are integral to the survival of many species including the monarch butterfly (Danaus plexippus) (Flockhart et al., 2014) it is important to understand the foraging behaviour of the milkweed plant’s primary predators.

Development of a human embryo comes about in three stages: blastulation, gastrulation, and neurulation. First, the egg and sperm fuse into a zygote composed of an internal plasma membrane and an external zona pellucida. The zygote develops into a morula by cleaving internally, dividing into multiple cells without gaining volume. The cells inside the zona pellucida start compacting and differentiation begins. A mass of embryoblasts develops at the centre of the zona pellucida surrounded by a layer of trophoblasts. The embryoblasts migrate to the top half of the cell, leaving behind an empty space known as the blastocoel. This stage marks the end of blastulation at which point the embryo is known as a blastocyst. Then, the embryoblast mass develops an inner cavity called the amniotic cavity. The layer of cells directly under the amniotic cavity differentiate into epiblasts and the layer of cells under the epiblasts become hypoblasts. Collectively, these two cell layers form the bilaminar disc. Next, a group of epiblasts known as the primitive streak form along the middle of the epiblast layer. These cells will migrate downwards past the epiblast layer to form a third layer between the epiblasts and hypoblasts. The three layers of this trilaminar disc are now known as germ layers. The topmost layer is the ectoderm, the middle layer is the mesoderm, and the bottom layer is the endoderm. The ectoderm will form the nervous system and the skin; the mesoderm will form the bones and muscles; and the endoderm will form the viscera. The creation of the three germ layers is known as gastrulation.

Identifying the number of plant species

    Our aim is to count the number of different plant species found around a series of local small aquatic ecosystems. 

    We intend to limit the radius within which we count the number of plant species to 2 metres into and 2 metres out of the pond or waterbed edge. Starting at an arbitrary point and marking it, the radius will be subdivided into 2 metre wide plots circling the entirety of the pond. This will be done in order to ensure accuracy of counting and to prevent backtracking. Within each of these plots, the number of plant species visible to the naked eye and the number of individuals of that species will be counted. Then, the counts for each species from each of the plots will be aggregated into a series of totals.

    The data will be analysed by generating a Simpson biodiversity index for each area of study. This is a statistical tool described by the following equation:

D = 1-[(n(n-1))/(N(N-1))]

Where n is the number of individuals of each species and N is the total number of individuals of all species, and D represents the biodiversity index. The higher D is, the higher the biodiversity of a particular area. 

    We expect the results to show the level of biodiversity around local small aquatic ecosystems in order to inform us about one aspect of the ecosystems’ integrities. As there is no data on the biodiversity of these ecosystems, we will have no point of comparison for our data.

Lastly, we chose to identify the green architecture already present around our focal bodies of water as a measure of the importance of green architecture in local construction projects. The hydrological environment of urban areas is markedly different from natural catchments, and is generally characterised by faster runoff process, shorter travel time for rainwater, and increased runoff volume (Sokac, 2019). Green rooves have served as the primary method employed to attempt to bring the hydrologic characteristics of urban environments closer to their natural counterparts (Cook, 2007). However, even though green rooves are often used to control runoff, their effectiveness has not been intensively researched (Berndtsson, 2010). Thus, we aim to document sustainable architecture structures around local small aquatic ecosystems: firstly in order to have another indirect measurement of their integrity, and secondly so as to determine whether or not local construction projects follow the trend of a growing importance of green building apparent in the construction market as a whole (Ahn & Pearce, 2007). 

One way of addressing a potential lack in flora diversity around local small aquatic ecosystems has been to plant non-invasive, sustainable species as per the recommendations of the EBVs employed by GEO BON (Haase et al., 2018). In order to remedy deficiencies in the matter economy, ILTER’s EI framework has suggested that sustainable ecosystem conditions could be reestablished by reducing excess runoff and subsequently abnormal levels of nutrients and other molecules like phosphate, nitrate, and ammonia (Haase et al., 2018). Green architecture has been used as a way of bringing an aquatic ecosystem closer to its natural hydrological conditions by creating structures that reduce anthropogenic impact on ecosystem hydrology (Cook, 2007). Some of these sustainable architecture developments include: green rooves, green streets, permeable paving, and the use of bioretention/ biofiltration materials and spaces (Cook, 2007; Davis, 2009). As these methods have been previously applied to reduce anthropogenic effects on ecosystem integrity, they are good candidates for potential ways of ameliorating the health of local small aquatic ecosystems.

Small aquatic ecosystems and wetlands are critical contributors to both freshwater biodiversity and ecosystem services (Williams et al., 2004; Verdonschot et al., 2011). In fact, ponds contribute the most to freshwater biodiversity, housing more species, more unique species, and more rare species than other small aquatic ecosystems (Williams et al., 2004). Only recently has this evidence come to light and with it has come a growing need to explore anthropogenic effects on small aquatic ecosystems, in order to reverse and prevent future damage to these oases of biodiversity (Biggs et al. 2016). Though the University of Massachusetts Amherst did collaborate with the MA Department of Environmental protection (MassDEP), MA Office of Coast Zone Management (MassCZM), and the Environmental Protection Agency (EPA) on a project to assess and monitor local aquatic ecosystem integrity, it was focused on forested wetlands, coastal salt marshes, and wadable fresh streams (web reference 1) and was designed to show that indices of biotic integrity (IBIs) could be developed directly from the empirical data (web reference 2). In this proposal we concentrate our research on ponds as their contribution to local biodiversity and anthropogenic stressors affecting their health have not yet been studied. We chose plant diversity as our first measure of ecosystem health due to it being a strong component of the biotic diversity parameter found in the ecosystem integrity (EI) framework (Müller, 2005) used by the European branch of the international long-term ecological research (ILTER) network to determine ecosystem health (Haase et al., 2018). In addition,the Group on Earth Observations Biodiversity Observation Network (GEO BON) that uses essential biodiversity variables (EBVs) (Haase et al., 2018) to monitor changes in biodiversity on a global scale uses plant diversity as a key taxonomic parameter to measure community diversity (Schmeller et al., 2018). Thus, since plant diversity is a point of intersection between the two major frameworks that aim to determine ecosystem health, it is likely to serve as a strong indicator of the health of the small aquatic ecosystems that are the focus of this study.

During human embryonic development, the brain forms from the walls of the neural tube. The human proto-brain is divided into four sections: the forebrain, the midbrain, the hindbrain, and the spinal cord. The forebrain is the largest section and forms two distinct structures, the telencephalon and the diencephalon. The telencephalon is the largest of the two and goes on to form the cortex that wraps around the diencephalon and midbrain sections in the fully developed brain. The diencephalon goes on to form the group of structures commonly known as the brain stem, composed of the thalamus, the hypothalamus, and the basal telencephalon. In addition to these grey matter structures, the developing brain forms the inner capsule. The inner capsule is a group of white matter - myelinated axon bundles - continuous with the cortical white matter that connects the thalamus to the cortex. Another important white matter structure is a commissure known as the corpus callosum that is an important link between the two hemispheres of the brain. The midbrain is made of the tectum and the tegmentum, which are responsible for a lot of auditory and visual reflexes. Through it runs the cerebrospinal aqueduct that transports cerebrospinal fluid (CSF) between the brain and spinal cord. As for the forebrain, the hindbrain can be split into two sections. The rostral-most section contains the cerebellum, our motor control centre, and the pons, which serves as a relay centre between the forebrain and the cerebellum. The caudal-most section contains the medulla, which switches signals between the body and the brain from ipsilateral to contralateral. Lastly, the spinal cord is composed of the dorsal horn, the intermediate zone, and the ventral horn. These grey matter structures are all involved in the relay of signals between the body and the brain. The dorsal horn is involved in signal reception, the intermediate zone is largely composed of interneurons and serves as a relay point, and the ventral horn is the location of efferent neurons that carry information to effector organs in the body such as muscles.

Development of a human embryo and its brain comes about in three stages: blastulation, gastrulation, and neurulation. First, the egg and sperm fuse into a zygote which has an internal plasma membrane and an external zona pellucida. The zygote cleaves internally, maintaining the same volume inside the zona pellucida but multiplying the number of cells inside it, at which point it is called a morula. The cells inside the zona pellucida go through compaction and differentiation starts to occur. A sphere of trophoblasts develops just under the zona pellucida and around the mass of embryoblasts inside the embryo. The embryoblasts then accumulate at the top half of the embryo, leaving a space called a blastocoel under them. This whole process is known as blastulation and the resulting structure is a blastocyst. Gastrulation follows blastulation first by the loss of the zona pellucida. Then, the mass of embryoblasts forms an inner cavity called the amniotic cavity. The cells under the amniotic cavity become epiblasts and the cells under the epiblasts become hypoblasts. These two cell layers are collectively known as the bilaminar disc. The primitive streak forms along the middle of the bilaminar disc, on the epiblast layer. This primitive streak is composed of epiblast cells migrating down and forming a middle layer of cells between the two original layers of the bilaminar disc. This forms a trilaminar disc with three layers known as germ layers. The topmost layer is the ectoderm, the middle layer is the mesoderm, and the bottom layer is the endoderm. The ectoderm will form the nervous system and the skin. The mesoderm will make the muscles and bones. The endoderm will make the viscera. The formation of these layers is known as gastrulation.

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