semans's blog

Plants differ from animals in many ways, one of which is the incidence of viable polyploidy. Ploidy refers to the number of chromosome pairs an organism has and polyploidy is the phenomenon wherein an organism will have more than one complete set of homologous chromosomes. Over 80% of flowering plants are polyploids, while the occurrence of animal polyploidy is a phenomenon of great rarity, almost absent in mammals and scarce in fish. One of the major reasons for this difference is the fact that plants rarely require a mate to create offspring, whereas animals often need a mate to produce viable offspring. Thus, should a polyploid animal mate with an animal of normal ploidy, it will create an aneuploidic zygote that cannot create viable gametes. Plants can undergo two kinds of polyploidization, allopolyploidization and autopolyploidization. Allopolyploidization occurs when two different species hybridize and the resulting offspring is viable and reproductively isolated. Autopolyploidization occurs when a plant species self fertilizes to create offspring that is reproductively isolated from its parent species. There are two major ways polyploidization can occur. The first is mitotic nondisjunction and can best be explained when observing allopolyploidization. When the haploid gametes of two different species hybridize, the resulting zygote has one chromosome of each kind, thus lacking homologous pairings. An error in mitosis can occur where the doubled chromosomes end up in the same daughter cell, thus yielding a diploid individual with two chromosomes of each type. The chromosomes in the new plant species can now synapse properly during meiosis and create viable haploid gametes that allow for self-fertilization. The second method involves meiotic nondisjunction. This type of nondisjunction can occur during meiosis I or meiosis II, but in both cases the result is diploid gametes. These diploid gametes can be fertilized by haploid gametes to yield nonviable triploid individuals, or they can fuse with another diploid gamete to create a viable tetraploid individual. So, if a plant produces two diploid gametes through nondisjunction and they self-fertilize, the result would be a new, tetraploid species. This species is now reproductively isolated from its parent as if the two were to mate they would create nonviable triploid individuals.

Moth and bat coevolution is a classic example of the intersection of behaviour and neurology. Bats locate their prey through echolocation, a process by which a bat emits ultrasonic waves and uses the reflection of the sound to locate itself in space and to find food. Bats have to eat at least once an hour to support their metabolism and so there is strong selection for bats that can echolocate efficiently. Similarly, moths are under heavy selection pressure to avoid becoming food. To sense the direction of their bat predators, noctuid moths possess two sensory nerves connected to their tympanum. The A1 nerve fires more frequently as ultrasonic sound gets louder and the A2 nerve only fires when ultrasonic sound is particularly intense. Each side of the moth thorax has a tympanum and its complementary pair of nerves. This allows the moth to determine the direction from which the bat is approaching. If the sound is louder on the right side than the left, then the moth knows the bat is coming from the right side. If the sound is louder when the moth has its wings up and softer when its wings are down, then the bat is coming from above. Within the three metre echolocating range of the little brown bat, its primary predator, the noctuid moth can sense the direction from which the bat is arriving and attempt to fly away from it. Should the bat get too close, the A2 nerves will fire causing the moth’s wings to beat out of sync and engaging the moth in a spiraling power dive. During this erratic movement, not even the moth knows where it will end up, though usually it will crash land in bushes that will mask its position. This evolutionary arms race is but one of many where there are heavy selection pressures on both predator and prey.

Plant pathology differs greatly from animal pathology. First and foremost, animals have an adaptive immune system that allows them to generate defences as new infections arise, but plants lack this capacity. Plants have a fixed immune system that either confers them resistance to a pathogen or doesn’t. Plant pathogens come in three general classes, necrotrophs, biotrophs, and hemibiotrophs. Necrotrophs are organisms that simply kill plant tissue upon infection using cellulase and hemicellulase, they tend to be generalists that can infect many plants. For biotrophs to go through their reproductive cycle they require live plant tissue and thus tend to infect specific hosts. Biotrophs will cause slowed senescence and will hijack plant cell machinery to generate metabolites for themselves rather than the plant. Lastly, hemibiotrophs are a mix between necrotrophs and biotrophs. In the first stage of their life cycle hemibiotrophs will act like biotrophs, hijacking plant tissue for their own purposes. In the second stage of their life cycle they will act as necrotrophs and kill the plant. Pathogens utilize three main ways of egress into a plant. They can either directly penetrate the plant through the use of a pilus or penetration cap, enter through pre-existing openings such as stomata, or enter through wounds. Plants have a series of defencive strategies to resist and counter infection. The first line of defence is physical, plants have a waxy cuticle and cell walls that aim to prevent direct access to plant cells. The second line of defence is specific, and is known as resistance (R) gene immunity that follows a gene for gene model. Pathogens produce effectors that aim to mask their presence, and plants produce proteins that are able to detect effectors. If a plant can produce a detector that recognizes even a single effector in a pathogen then it can defend against it, otherwise the plant will be infected. The methods of defence include production of toxins that kill the pathogen, synthesis of papillae to reinforce the cell wall, and a hypersensitive response that involves rapid cell death around the area of infection.

Cell expansion and growth occurs very differently in plants than it does animals. Animals tend to produce unique organs with specific cells for each organ, whereas plant growth is iterative and will generate many of the same organs. Stem cell tissue in plants is known as meristem and contains undifferentiated cells. There is a shoot apical meristem and root apical meristem both of which are responsible for primary growth, such as new leaves, flowers, and roots. The other kind of meristem found in the cambium is responsible for the growth of bark, xylem, and phloem. The basic structure of the apical meristems is a stacked one. The first level is at the apex of the meristem and consists of the newly dividing cells; the second level just below is where cell elongation takes place; underneath it, the third level is where cell differentiation occurs; and the last level below that is where mature cells are located. The cell division layer leads to the creation of new cells with primary cell walls that will generate leaves and flowers. The second level during which cell elongation occurs is a dynamic layer. Plant cells have the capacity to increase their solute potential by generating an electrostatic gradient that powers active transport channels that move metabolites and ions in the cell. Water can then enter the plant cells via osmosis or aquaporins. This raises the internal pressure of the plant cell - known as turgor pressure - which pushes against the primary cell wall causing it to expand. Some parts of the primary wall are less rigid than others, causing directional expansion, usually lengthwise. Eventually the pressure exerted on the primary cell wall equalizes with the pressure the wall exerts on the cell’s plasma membrane and expansion comes to a halt. At this point, the cells will begin to differentiate by synthesizing a variety of secondary cell walls that will determine their purpose. Once this process is done, the cells have fully differentiated and can now form the new organs of the plant.

Vertebrate hearing has been the subject of much study. The anatomy of the vertebrate ear is complex, but can be subdivided into three general regions, the outer ear, the middle ear, and the inner ear. The outer ear consists of the pinna and a duct that leads to the middle ear. The pinna’s primary function is amplification, allowing for sounds dispersed over the large surface area of the ear to be channeled into a small air duct towards the middle ear. The middle ear converts this sound energy into mechanical energy via the tympanic membrane. The distance this membrane is stretched is a function of the sound’s amplitude, the number of times per second the membrane is stretched from crest to trough is a function of the sound’s frequency. The shifts in the tympanic membrane are translated into three ear ossicles that function like a lever, amplifying the sound as it travels to the entrance of the inner ear, the oval window. The oval window is a membrane on the cochlea that vibrates in response to the last ossicle’s movement and translates this mechanical energy into hydraulic energy. The frequency of the sound is translated by how quickly the liquid revolves through the cochlea and sound amplitude is translated by the amount of compression applied to the fluid. Translation of this movement into sound perception is done through the organ of Corti, a series of membranes and special nerve cells called hair cells. The organ of Corti is composed of two membranes, the lower basilar membrane which is flexible, and the upper tectorial membrane which is more rigid. Lodged into the basilar membrane are the bottom ends of the hair cells, whose namesake hair-like protrusions stick out at the top and into the tectorial membrane. The basilar membrane will resonate based on the movement of the fluid, which is passed on to the hair cells through their axonal projections. Sound amplitude is translated by the amount these hair cells move, and hence the amount of neurotransmitter they release into the tectorial membrane, the more neurotransmitter, the louder we perceive that sound. Sound frequency is more complicated. The stiffness of the basilar membrane differs at its base and at its apex. The basilar fibres are shorter and stiffer at the base, while longer and more flexible at the apex. Higher frequency sounds cause the shorter fibres to vibrate and lower frequency sounds cause the longer fibres to vibrate. An animal’s hearing range increases as the difference between basal and apical fibre length increases. The shorter the fibre, the higher the frequency that can be heard, the longer the fibre, the lower the frequency that can be heard.

The lack of neuron staining techniques prior to the Nissl stain and the Golgi stain. Though Nissl’s technique came first, it only revealed neurons’ endoplasmic reticulum and parts of the cell body. It was only until Camillo Golgi developed his staining method, first known as the “black reaction”, that neurons as a whole were revealed. This was a groundbreaking technique that led to decade long debates about the nature of the nervous system, especially as to whether neurons were contiguous or separate. Since then, staining techniques have evolved to allow imaging of anything from axonal networks to individual neuropeptides. The Weigert-Weil stain enables us to visualise the myelin sheath of axons, giving us the opportunity to observe how connections are established throughout the brain. Modern techniques like in-situ hybridization (ISH) allow us to see which genes are expressed in a sample of neurons. The first step in ISH involves binding a labelled mRNA strand complementary to the mRNA produced by the gene of interest. The second step involves the introduction of a primary antibody with a variable region keyed to the mRNA label binds to the mRNA strand. The final step is injection of fluorescently labelled secondary antibodies with variable regions that recognize the species-specific heavy chain of the primary antibodies, and then imaging the cells with the appropriate wavelength of light. This technique allows scientists to know which neurons are expressing the gene of interest. Another modern staining method called immunohistochemistry (IHC) is also an antibody stain that uses fluorescently labelled antibodies to visualise certain molecules. However, as opposed to ISH, IHC reveals the presence of proteins such as neuropeptides, which can also be indicative of neuronal function.

The history of neurology is a fragmented one fraught with disagreements, propositions, and rebuttals, often taking two steps forward and one step back. The earliest evidence of brain surgery dates back to prehistoric skulls with the marks of trepanation and subsequent recovery. Many millennia later in 400BCE, the Ancient Greeks discovered the separation between the central nervous system (CNS) and peripheral nervous system (PNS), though opinions were split as to the function of the brain. Two hundred years later, Galen of Ancient Rome found cerebrospinal fluid (CSF) in sheep skulls and, in the current of the bodily humours popular at the time, concluded that it was this liquid that gave rise to the conscious mind. Records of brain research in the Occident end there for nearly 1700 years, until the 16th century. During the Renaissance, Leonardo da Vinci restarts the study of brain anatomy and makes detailed drawings of the brain and its ventricles. In the mid-1500s, Andreas Vesalius dissects the bodies of executed prisoners and refutes Galen’s hypothesis that CSF is the seat of consciousness, claiming that the brain matter gives rise to the mind. However, in the 1600s, Descartes counters Vesalius’ theory in saying that the mind and brain are separate entities, thus giving birth to Dualism. This idea wouldn’t last long in the field of neurology as Willis and Wren’s study of brain anatomy led them to the same conclusion as Vesalius, brain matter not CSF holds human consciousness. Many small discoveries over the next centuries resulted in the discovery that nerves communicate via electricity and that different parts of the brain are responsible for different functions. The functional unit of the brain, the neuron, was only discovered in the 1900s when they were stained by Camillo Golgi. For decades Golgi and his colleague Santiago Ramon y Cajal would debate neuronal function. Golgi favoured the idea that neurons formed a contiguous system while Cajal hypothesized that neurons were separable, discrete units. Finally, as we approach the 21st century, the advent of the electron microscope vindicated Cajal’s theory. Neurons are in fact the basic unit of the brain and, though separate, they communicate via synapses.

Figure 1. A close-up image of an orchid. The flower shows two sterile whorls, the outer whorl has three sepals and the inner whorl has three petals. "Orchid" flickr photo by gssavage https://www.flickr.com/photos/gssavage/4696302471 under a Creative Commons (BY-ND) license.

The history of neurology is a fragmented one fraught with disagreements and centuries of stagnation. The earliest evidence of brain surgery dates back to prehistoric skulls with the marks of trepanation and subsequent recovery. Ancient Egyptians suggested that the heart was the seat of the soul rather than the brain. After that, the Ancient Greeks discovered the separation between the central nervous system (CNS) and peripheral nervous system (PNS), though opinions were split as to whether the brain matter actually served a purpose in consciousness. Later, in 200BCE, Galen of Ancient Rome discovered cerebrospinal fluid in sheep and concluded that it was this liquid that gave rise to the conscious mind. Records of brain research in the Orient end there for nearly 1700 years, until the Renaissance in the 16th century. Leonardo da Vinci picks up the study of brain anatomy and makes detailed drawings of the brain and its ventricles. Slightly later in the mid 1500s, Andreas Vesalius dissects the bodies of executed prisoners and refutes Galen’s hypothesis that CSF is the seat of consciousness, rather, the solid matter gives rise to the mind. However, in the 1600s, Descartes counters this hypothesis in saying that the mind and brain are separate entities, giving birth to philosophical dualism. But, around the same time, Thomas Willis and Christopher Wren dissect human bodies and come to the same conclusion as Vesalius, the wellspring of the mind is not CSF but brain matter. Many small discoveries over the next centuries resulted in our understanding that nerves communicate via electricity and that different parts of the brain are important for different functions. It was only in the early 1900s that neurons were stained (Camillo Golgi) and then hypothesized to be the individual units of the brain (Santiago Ramón y Cajal). Finally, as we approach the 21st century, research has brought to light the existence of different neuron types, and other classes of brain cells - such as glia - that serve a host of other purposes in maintaining brain function. Though we know much about the anatomy of the brain, we are still in the dark about its generation, possible regeneration, information processing capabilities, and how it gives rise to consciousness.

The uniformity of most modern crops is due to three genetic bottlenecks that took place during centuries of plant domestication. The first occurred at the start of sedentary, agricultural life, and could best be described as the domestication bottleneck. Early farmers only used a limited number of individuals as the progenitor species for their crop, resulting in a landrace. Thus, all of the subsequent crop plants came from the few those farmers had picked out, narrowing genetic variation in that plant. The second occurred during the first migratory phases of human civilization. When people migrated to new lands they would bring with them only a select number of plants from the landraces, which would once again reduce the genetic variation in the resulting crops. Finally, the third occurred many centuries later with the advent of modern genetic technology. Through the use of gene editing technology it became possible to create homogeneity for entire crop fields. Plants could now be edited to include genes of choice such as herbicide resistance, pest resistance, disease resistance, and many other traits, some of which allowed for the complete mechanization of farming. The final bottleneck has resulted in single plant genotypes propagated across entire fields, random variations becoming a thing of the past.