Here's the article:
Clark, Ryan. “The Past, Present, and Future Hydrology of Devereux Slough.” CCBER, May 4, 2017. https://www.ccber.ucsb.edu/news-events/past-present-and-future-hydrology-devereux-slough.
Wednesday, February 26, 2020
Some neat info about Devereux
Hey everyone! In case you weren't aware, Devereux Slough is pretty neat. If you, like me, weren't aware of its existence until this quarter, here's some great reading from a CCBER blog about Devereux's hydrology. If you're unfamiliar with estuarine systems like Devs, this is a great read to gain some insight into the water sources feeding the Slough. Additionally, Devereux has also been the site of a massive restoration project headed by NCOS, which you can also get involved in. Also, and most importantly, Devereux is pretty much at full capacity right now and could break into the ocean at pretty much any point. If you get really lucky and spend a lot of time there, you might be able to witness this really neat phenomenon, so it's a great excuse to get out and see the slough!
Monday, February 17, 2020
The Food Switch and Coxsackievirus
Hi everyone!
Came upon a fun read about how the food we eat can have effects on our susceptibility to coxsackievirus and pancreatitis. For reference, coxsackieviruses belong to a category of viruses known as enteroviruses, which are characterized by having no other known animal reservoir (besides humans) and persistence in the human population, as they have a low ability to cause harm and are often attenuated (weakened.)
Seeing as they don't have any other known reservoirs, it is suspected that enterovirus infections stem from outside causes, such as environmental factors. In this paper, they discuss the effects of malnourishment/food restriction (FR) on susceptibility of CVB3 (cocksackievirus type B3) infection by conducting studies on mice; results showed that the mice that developed marasmus (severe weight loss from FR) showed higher levels of virus once infected in comparison to mice fed on a normal diet. However, susceptibility significantly decreased if the FR mice were fed during time of infection, leading researchers to believe in the existence of a "switch" that acts quickly in the presence of food against CVB3 infection.
They do discuss the effects of on autophagy (the process of removing unnecessary or damaged cellular components) but the focus was primarily about how susceptibility is altered when food is restricted. I'm curious to see the prevalence of enteroviral infections around the world, and if malnourishment is the central reason for it, or if there is a more significant environmental issue present responsible.
https://www.tandfonline.com/doi/full/10.1080/15548627.2020.1720425
Came upon a fun read about how the food we eat can have effects on our susceptibility to coxsackievirus and pancreatitis. For reference, coxsackieviruses belong to a category of viruses known as enteroviruses, which are characterized by having no other known animal reservoir (besides humans) and persistence in the human population, as they have a low ability to cause harm and are often attenuated (weakened.)
Seeing as they don't have any other known reservoirs, it is suspected that enterovirus infections stem from outside causes, such as environmental factors. In this paper, they discuss the effects of malnourishment/food restriction (FR) on susceptibility of CVB3 (cocksackievirus type B3) infection by conducting studies on mice; results showed that the mice that developed marasmus (severe weight loss from FR) showed higher levels of virus once infected in comparison to mice fed on a normal diet. However, susceptibility significantly decreased if the FR mice were fed during time of infection, leading researchers to believe in the existence of a "switch" that acts quickly in the presence of food against CVB3 infection.
They do discuss the effects of on autophagy (the process of removing unnecessary or damaged cellular components) but the focus was primarily about how susceptibility is altered when food is restricted. I'm curious to see the prevalence of enteroviral infections around the world, and if malnourishment is the central reason for it, or if there is a more significant environmental issue present responsible.
https://www.tandfonline.com/doi/full/10.1080/15548627.2020.1720425
Sunday, February 16, 2020
Fog in the California redwood forest: ecosystem inputs and use by plants
Fog is probably one of the most underrated phenomenons. Sure, it may cause traffic during the morning, but its benefits to coastal ecosystems outweighs human issues. Inspired by the redwoods in Santa Barbara (check them out at the SB Botanical Garden!) and the discussion of gymnosperms in class, I decided to look more into just how significant fog is to a coastal ecosystem full of gymnosperms.
Fog is present in multiple ecosystems throughout the world and contributes to a significant fraction of total hydrologic input, particularly in coastal areas that hardly receive rainfall (Dawson, 1998). Fog contributes to ecosystem biogeochemistry and may be the only source of water for plants growing under the redwoods. The researcher, Dawson, set out to quantify how present fog is in the ecosystem by analyzing the xylem tissues of plants under the redwoods. This data provided which water sources the plants were using. This was determined by analyzing the different types of isotopes in water. Fog is isotopically enriched in the heavier isotopes 2H and 18O (Dawson, 1998).
Dawson found that the plants under the redwoods absorbed more of the fog that fell from the redwood canopy. 66% of the water in the plants under the redwoods came from the fog water than had dripped down from those redwoods. Lots of these plants were adapted to maximize fog absorption by having specialized water entry in their leaves, unique rooting patterns and depths, and the ability to proliferate their roots (Dawson, 1998). It is really interesting to read how these plants are able to adapt to fog. I look forward to reading more on how the life cycle of redwoods is impacted by fog once we continue our discussion of gymnosperms in lecture.
Citation:
Dawson, T. Fog in the California redwood forest: ecosystem inputs and use by plants. Oecologia 117, 476–485 (1998). https://doi.org/10.1007/s004420050683
Exaptation versus adaptation
Back during our in class writing assignment, I wrote about the differences between the use of the terms "exaptation" and "adaptation," from lecture during week 2. Since then, I updated it a little and decided to post the current version today. Here it is:
Ever since the term “exaptation” was coined, it has inevitably been compared to the more common term of “adaptation.” Exaptation refers to a character that was initially developed for one purpose, but has since been used in a different way. One example proposed by some ecologists is that the warning colors indicating that an animal would be toxic to eat, such as on the Monarch butterfly, was originally a trait developed for sexual selection and mating preferences.
Many scientists have begun to argue that all adaptations could be described as exaptations, if you look far enough back in time. And therefore, no adaptations are exaptations, because they are all simply adaptations. Larson (2013) argues that a better use for the term exaptation is within its application to the ever-changing realm of technology. The transition between the typewriter and computer is simple in terms of word processing and the ability to write faster. But, the subsequent developments of all that computers are used for now is remarkable.
My research involves bees and plant-pollinator interactions. The differences between and within the six families of bees are astounding, and their behavioral differences make sense of these physical differences. However, to try to go back in time from today’s perspective and determine which traits were caused by adaptation and which were caused by exaptation seems illogical. In this light, I would argue that adaptation makes sense to use overall, but when describing or discovering changes happening today, exaptation may fit and be used accurately.
These differences are largely for semantic debate, as the act of describing a species today really only requires a word like “adaptation.” However, through the accurate use of the term “exaptation,” there is some room for more knowledge and description of current processes in some of the changes happening today.
Source: Larson, G, Stephans, P, Tehrani, J & Layton, R 2013, ‘Exapting Exaptation’, Trends in Ecology & Evolution, vol. 28, no. 9, pp. 497-498.
Ever since the term “exaptation” was coined, it has inevitably been compared to the more common term of “adaptation.” Exaptation refers to a character that was initially developed for one purpose, but has since been used in a different way. One example proposed by some ecologists is that the warning colors indicating that an animal would be toxic to eat, such as on the Monarch butterfly, was originally a trait developed for sexual selection and mating preferences.
Many scientists have begun to argue that all adaptations could be described as exaptations, if you look far enough back in time. And therefore, no adaptations are exaptations, because they are all simply adaptations. Larson (2013) argues that a better use for the term exaptation is within its application to the ever-changing realm of technology. The transition between the typewriter and computer is simple in terms of word processing and the ability to write faster. But, the subsequent developments of all that computers are used for now is remarkable.
My research involves bees and plant-pollinator interactions. The differences between and within the six families of bees are astounding, and their behavioral differences make sense of these physical differences. However, to try to go back in time from today’s perspective and determine which traits were caused by adaptation and which were caused by exaptation seems illogical. In this light, I would argue that adaptation makes sense to use overall, but when describing or discovering changes happening today, exaptation may fit and be used accurately.
These differences are largely for semantic debate, as the act of describing a species today really only requires a word like “adaptation.” However, through the accurate use of the term “exaptation,” there is some room for more knowledge and description of current processes in some of the changes happening today.
Source: Larson, G, Stephans, P, Tehrani, J & Layton, R 2013, ‘Exapting Exaptation’, Trends in Ecology & Evolution, vol. 28, no. 9, pp. 497-498.
Monday, February 10, 2020
Ocean Beach Cleanup @ Stearns Wharf
Hi everyone,
I'm a volunteer at the Santa Barbara Sea Center and we're hosting an ocean beach cleanup at Stearns Wharf in downtown SB on February 26 from 2:30-4:30 pm. You can bring friends, and it's a great opportunity to get out in the sun and help keep the coasts clean! You can also potentially get community service hours from it as well.
Let me know if you're interested in volunteering and cleaning up the coast!
I'm a volunteer at the Santa Barbara Sea Center and we're hosting an ocean beach cleanup at Stearns Wharf in downtown SB on February 26 from 2:30-4:30 pm. You can bring friends, and it's a great opportunity to get out in the sun and help keep the coasts clean! You can also potentially get community service hours from it as well.
Anyone who is interested can either sign up at https://www.eventbrite.com/e/
Let me know if you're interested in volunteering and cleaning up the coast!
Saturday, February 8, 2020
Sloth Hair and the Drug Industry: An Oddly Fascinating Pairing
For those of us who dabble in sloth ecology, or simply enjoy learning about the slow-going creatures, it is not particularly surprising that there is more to the hot topic of CS Bio 30 Week 4 than cyanobacteria interactions and an inability to perform excretory activities in trees. While sloths are not exactly a physician's first thought when treating patients with cancer, a group of biologists have asserted that sloths should not be overlooked by pharmaceutical companies in the development of new bioactive drugs.
In their 2014 study, Higginbotham et al. collected and cultured fungi from coarse hair samples from a group of 3-toed sloths in Panama. Using PCR techniques to extract genomic DNA from the fungi, as well as BLAST and GenBank comparisons, the authors were able to identify 84 different fungal isolates in the hair of these 3-toed sloths. 84 different isolates! Of course, that raw data itself is pretty wild, but the key bit is in the bioactivity findings. Higginbotham et al. (2014) defined an isolate to be very bioactive if it was responsible for at least a 50% decrease in the growth of cancer cells or parasites in vitro. Overall, sixteen fungi proved to be highly bioactive in at least one bioassay. Fifteen of those fungi were highly inhibitory of the growth of MCF-7 breast cancer cells. One extract also had high bioactivity against a strain of Gram-negative bacteria, which is a cool connection to our past prokaryotic diversity discussion.
As a whole, though this study is a bit of a dry and statistical read through the middle and is not published in the most well-known journal, it illustrates a very niche realm of ecology and microbiology with some rather interesting and exciting implications. The notion that we may be able to discover new microorganisms in sloth hair that could one day provide new treatments for neglected tropical diseases and certain cancers is something I would have never considered prior to reading this article.
Link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084549
Citation:
Higginbotham, S., Wong, W.R., Linington, R.G., Spadafora, C., Iturrado, L., et al. (2014). Correction: Sloth Hair as a Novel Source of Fungi with Potent Anti-Parasitic, Anti-Cancer and Anti-Bacterial Bioactivity. PLOS ONE, 9(1). doi: 10.1371/annotation/10c47668-8c49-48d2-ba65-60420af463b6.
In their 2014 study, Higginbotham et al. collected and cultured fungi from coarse hair samples from a group of 3-toed sloths in Panama. Using PCR techniques to extract genomic DNA from the fungi, as well as BLAST and GenBank comparisons, the authors were able to identify 84 different fungal isolates in the hair of these 3-toed sloths. 84 different isolates! Of course, that raw data itself is pretty wild, but the key bit is in the bioactivity findings. Higginbotham et al. (2014) defined an isolate to be very bioactive if it was responsible for at least a 50% decrease in the growth of cancer cells or parasites in vitro. Overall, sixteen fungi proved to be highly bioactive in at least one bioassay. Fifteen of those fungi were highly inhibitory of the growth of MCF-7 breast cancer cells. One extract also had high bioactivity against a strain of Gram-negative bacteria, which is a cool connection to our past prokaryotic diversity discussion.
As a whole, though this study is a bit of a dry and statistical read through the middle and is not published in the most well-known journal, it illustrates a very niche realm of ecology and microbiology with some rather interesting and exciting implications. The notion that we may be able to discover new microorganisms in sloth hair that could one day provide new treatments for neglected tropical diseases and certain cancers is something I would have never considered prior to reading this article.
Link: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084549
Citation:
Higginbotham, S., Wong, W.R., Linington, R.G., Spadafora, C., Iturrado, L., et al. (2014). Correction: Sloth Hair as a Novel Source of Fungi with Potent Anti-Parasitic, Anti-Cancer and Anti-Bacterial Bioactivity. PLOS ONE, 9(1). doi: 10.1371/annotation/10c47668-8c49-48d2-ba65-60420af463b6.
Wednesday, February 5, 2020
Does the lightness in your eyes affect ability to cope with seasonal depression??
For the fourth week of CSBIO20, I decided to read about human pigmentation and selection based on environmental factors. In a 2012 study conducted by Richard Sturm and David Duffy ("Human pigmentation genes under environmental selection"), they explored how environmental changes have influenced pigmentation genes as humans have dispersed around the world. While skin, hair, and eye color do have a lot of variation within one anther, all three genes are related. Through the Human Genome Diversity Panel, individuals submitted genetic data for scientists to look at ancestry informative markers. In this study, researchers looked at nine climate variables that had an effect on human physiology using demographic history.
Sturm and Duffy found a lot of interesting results when comparing many different genes across the globe; for example, the MC1R allelic diversity was generally lower in Africa and higher in Europe. Furthermore, an allelic mutation OCA2, which causes full albinism, was found in the Polynesian Islands, and it is supposed to have come from genetic drift resulting from the population founder effects stemming from human dispersal. One element of skin selection this study explored was accumulation of melanosomes in keratinocytes, which can help adaptation of UV radiation protection, energy transport and drug binding advantages, as well as hearing and sight aid. One of the selective pressures explaining this accumulation seemed to be need for Vitamin D synthesis. Scientists have not yet found evidence for immune system selection in global populations in a pigmentation gene.
One of the aspects of this study I found particularly interesting was that in Europe, eye color may have been sexually selected for, and it was at one point believed that people with blue eyes may have been better selected to withstand the dark days of winter because of the lightness in their eyes.
Overall, there has been large amounts of selection when it comes to human pigmentation, much of which stemming from the environment. It will be incredibly interesting to see how human pigmentation and phenotypic representations change in an ever-changing world.
Sturm, R.A., Duffy, D.L. Human pigmentation genes under environmental selection. Genome Biol 13, 248 (2012). https://doi.org/10.1186/gb-2012-13-9-248
Sturm and Duffy found a lot of interesting results when comparing many different genes across the globe; for example, the MC1R allelic diversity was generally lower in Africa and higher in Europe. Furthermore, an allelic mutation OCA2, which causes full albinism, was found in the Polynesian Islands, and it is supposed to have come from genetic drift resulting from the population founder effects stemming from human dispersal. One element of skin selection this study explored was accumulation of melanosomes in keratinocytes, which can help adaptation of UV radiation protection, energy transport and drug binding advantages, as well as hearing and sight aid. One of the selective pressures explaining this accumulation seemed to be need for Vitamin D synthesis. Scientists have not yet found evidence for immune system selection in global populations in a pigmentation gene.
One of the aspects of this study I found particularly interesting was that in Europe, eye color may have been sexually selected for, and it was at one point believed that people with blue eyes may have been better selected to withstand the dark days of winter because of the lightness in their eyes.
Overall, there has been large amounts of selection when it comes to human pigmentation, much of which stemming from the environment. It will be incredibly interesting to see how human pigmentation and phenotypic representations change in an ever-changing world.
Sturm, R.A., Duffy, D.L. Human pigmentation genes under environmental selection. Genome Biol 13, 248 (2012). https://doi.org/10.1186/gb-2012-13-9-248
Marine Community Connectivity
For week 5 of CSBIO20, I read an article in the Journal of Applied Ecology published extremely recently in January 2020. It discussed marine spatial systems in terms of both natural and artificial connectivity of communities in the North Sea. To understand marine environments and ecosystems, one must take into account changing environmental pressure as well as increasing anthropogenic pressures such as oil rigs, fishing, etc. To improve marine ecosystem resilience, effective management with MPAs and other procedural systems is crucial.
In this particular article, researcher Hannah Tidbury looked at how marine space changes due to hard structures and natural structures changing. More specifically, new regulations in the North Sea region have led to many artificial structures residing in the marine system being removed; Tidbury looked at the effects of these removals on marine community ecology. One issue her team faced was a lack of empirical data already available, so she set out to comprise some usable data using social network analysis in a new way to help provide some interpretable data for management.
To conduct this study, she looked at larval dispersal scores over a course of ten years for seven different marine species, then established each species' community establishment potential. Ultimately, they found weaker connectivity when it came to artificial structure, but still a lot of connectivity there. Even with the removal of some artificial structures in the North Sea, connectivity in the natural areas remained stable; however, artificial structures do provide the connectivity in places where no substrate exists - it bridges the gaps.
This study expressed extremely new ideas because connectivity is difficult to evaluate, social network analysis (with the larvae dispersal) is not typically used in this context, and general understanding of marine connectivity is limited. Ideally, management for marine systems can better understand things like community connectivity before making decisions like removing artificial structures in the North Sea. For example, if they remove an oil rig, this removal may allow more recreational or fishing vessels in that area to disrupt connectivity.
, , , et al. Social network analysis as a tool for marine spatial planning: Impacts of decommissioning on connectivity in the North Sea. J Appl Ecol. 2020; 00: 1– 12. https://doi-org.proxy.library.ucsb.edu:9443/10.1111/1365-2664.13551
In this particular article, researcher Hannah Tidbury looked at how marine space changes due to hard structures and natural structures changing. More specifically, new regulations in the North Sea region have led to many artificial structures residing in the marine system being removed; Tidbury looked at the effects of these removals on marine community ecology. One issue her team faced was a lack of empirical data already available, so she set out to comprise some usable data using social network analysis in a new way to help provide some interpretable data for management.
To conduct this study, she looked at larval dispersal scores over a course of ten years for seven different marine species, then established each species' community establishment potential. Ultimately, they found weaker connectivity when it came to artificial structure, but still a lot of connectivity there. Even with the removal of some artificial structures in the North Sea, connectivity in the natural areas remained stable; however, artificial structures do provide the connectivity in places where no substrate exists - it bridges the gaps.
This study expressed extremely new ideas because connectivity is difficult to evaluate, social network analysis (with the larvae dispersal) is not typically used in this context, and general understanding of marine connectivity is limited. Ideally, management for marine systems can better understand things like community connectivity before making decisions like removing artificial structures in the North Sea. For example, if they remove an oil rig, this removal may allow more recreational or fishing vessels in that area to disrupt connectivity.
, , , et al. Social network analysis as a tool for marine spatial planning: Impacts of decommissioning on connectivity in the North Sea. J Appl Ecol. 2020; 00: 1– 12. https://doi-org.proxy.library.ucsb.edu:9443/10.1111/1365-2664.13551
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