Thursday, March 10, 2016

Break It Down!: Taphonomic Factors Affecting Parasite Preservation

Greetings Fellow Parasitophiles!

Today, is an exciting day for's the day that I sent my dissertation manuscript off to my supervisory committee for approval before I defend my dissertation here in a few weeks! (Things are getting very, very real!) In celebration of this occasion, I decided to allow myself more writing! (I really am a bit of a nerd sometimes...well, most of the time...and more than a bit...) In trying to decide what to share with all of you, I realized that I had not yet posted about my most recent paper. So, here it is! My first paper of 2016 and the story behind it!

I remember sitting at coffee one Friday, as I do with my advisor for our weekly lab meetings, and discussing some of the various factors that affect the preservation of parasite eggs in archaeological materials. We talked about both the abiotic (non-living) factors, like soil pH and climate, and some of the biotic (living) factors, like the actions of decomposer species. My advisor turned to me and said something along the lines of, "you should write a paper on that sometime".

I found the idea intriguing and thought about it a lot over the next few months. I started working on a manuscript without a clear idea of where I would go with the paper. I thought about how to categorize the major contributing factors that affect the preservation of parasite eggs in both positive and negative ways. I eventually came up with five broad categories of taphonomic (taphonomy is the study of decomposition and preservation) factors that affect parasite eggs existing in archaeological contexts. Those five broad categories were as follows:

[From Morrow et al., 2016]

1) Abiotic Factors--Those non-living things that influence preservation, such as temperature, soil conditions, and the chemical environment in which archaeological materials are found.

2) Contextual Factors--Those reflecting the archaeological context from which we collect parasite data. (i.e. parasite eggs in mummies preserve differently than those in coprolites or latrines)

3) Anthropogenic Factors--Those arising from the interactions humans have with the deposition, manipulations, excavation, transportation, and analyses of archaeological materials.

4) Organismal Factors--Those inherent in the biology of the organisms you are studying, such as the features of an egg that make them more susceptible to degradation or the natural history of a parasite that makes it more likely to be recovered from human feces.

5) Ecological Factors--Those involving the interactions of parasite evidence with other organisms, like decomposers, predators that my ingest parasite eggs, or vectors than can transport the eggs from one fecal deposit to another.

Each of these broad categories could be further subdivided into other categories and can affect the preservation of parasites in both positive and in negative ways. To provide examples of how these factors affect parasite egg preservation, we presented three case studies and discussed these five categories of taphonomic agents for each case.

I won't go into case-by-case detail (you are more than welcome to read the paper if you are interested in that bit), but I will tell you a bit about the three cases. These sites were each near and dear to my heart as they were the first three things that I published about. (One in a special historical journal that hasn't come out yet and two peer-reviewed articles that I talked about in previous posts here and here.)

Case 1: The recovery of intestinal parasites from historic mummies in Vilnius, Lithuania. In the first paper about these parasites, we highlighted a taphonomic issue that only arises with the analysis of mummies.

Case 2: The recovery of intestinal parasites from coprolites recovered from medieval skeletonized burials in Nivelles, Belgium. In the original publication of this material, we discussed an instance of extreme parasitism revealed by the analysis of coprolites from one one of the burials.

Case 3: The lack of parasites recovered during the analysis of embalming jar contents from crypts containing members of the famed Medici family of Florence, Italy. The potential reasoning for the lack of parasite evidence was discussed at great length in the original paper (which is still "in press" after several years). These reasons ranged from taphonomic to cultural in nature and included a discussion of how Medici affluence likely played a role in reducing the risk of parasite infections and in providing the most effective treatments of the time to control for infections had they occurred.

Each of these studies demonstrated a range of taphonomic considerations for the interpretation of archaeoparasitological data. This paper concludes with a discussion of how important it is for researchers to consider taphonomic factors when they discuss their findings. It urges future studies to discuss the five broad categories of taphonomic factors that may have positively or negatively affected the preservation of their parasite eggs.

I have to say that this is probably my favorite paper to have ever published. I love how it turned out. I was happy to have run with a simple suggestion (which my advisor may or may not have expected me to actually follow through with so quickly) and to have created an article that is actually really important for the advancement of the field. I got to work with an undergraduate as a mentor and I got to publish with an international colleague. I feel that this experience has helped me to grow in many ways professionally and I am proud to have such an elegant paper to show for it.

The Moral of the Story
When your advisor gives one of those small comments like, "you should do...." don't brush it off and put it on your list of things to do after you graduate. Take a little time to assess whether or not you could actually gain a lot from working on something might end up with something that is much bigger than you had originally thought it would be! Also, don't let your dissertation be the only thing that you leave with when you graduate. You are much more marketable if you can show that you have the ability to do other things!

Title Shot!

Saturday, February 27, 2016

Sharing Poop and Parasites

I've missed writing to you guys...dissertation and general life has been a little OP lately. (OP = "over powered"'s a slang term used often in the gaming world and I've been married to a gamer for too long to not use it.) I won't waste time saying that this is me starting up regular posts again, the dissertation is still not finished (though I'm getting close!) and I have a pretty busy few months ahead of me. I'm hoping to start back up this summer, after I (FINALLY) graduate, but I'm not making any promises just yet.

Today, I'm writing to you for a different reason. I recently competed in an Elevator Speech Competition hosted by my school. I had a bit of a rough time with delivery, but in the end it wasn't all bad. For this competition, I was given 1 slide (with no moving animations) and three minutes to tell a general audience about my research. For those interested, I've included the slide and a transcript of my speech below. Happy reading!

My Elevator Speech

Poop and parasites; two things that I love despite what other people think. Though not always appropriate dinner conversation, poop provides a wealth of data regarding diet and disease. This is as true for what many of you made earlier today as it was for humans thousands of years ago.

My dissertation focuses on retrieving data from 1,300-year-old paleo-poops known as “coprolites”, like the one in the middle of this slide. By analyzing coprolites, we are able to reconstruct diets and patterns of parasite infections that occurred in pre-history. This allows us to better understand the origins of human-parasite associations that still affect people in the modern world.

The coprolites that I work with come from a cave in Mexico known as “La Cueva de los Muertos Chiquitos”. This cave held hundreds of coprolites that were sealed beneath two adobe floors, making for some of the best-preserved parasite evidence in the world…now that’s the kind of high-quality crap that we archaeoparasitologists dream about!

The diversity of parasites recovered from this site is amazing. Starting at 12 o’clock, we see a Physaloptera egg, which is associated with dogs. Moving clockwise we see a human whipworm egg, then at 4 o’clock we see Toxascaris, another dog parasite that infects humans from time to time. At 6 o’clock are the results of a molecular test used to look for parasites that don’t leave behind eggs. Ignoring the control wells on the top left, every place that you see yellow represents a positive sample for a diarrhea-inducing parasite called Cryptosporidium parvum. Moving along, the egg you see at about 7 o’clock belongs to a tapeworm and the green egg is that of a human pinworm. Finally, the one up there at about 10 o’clock is a fluke egg. Each of these parasites has a distinct life cycle involving different hosts and modes of transmission.

By recovering parasite data, we are able to infer patterns of human behavior, for example, the dog parasites I mentioned tell us that the people using this cave had close associations with dogs and the molecular test at 6 o’clock tells us that lots of people had diarrhea. The pinworm eggs were so prevalent among the coprolites that we know the vast majority of people at this site were infected.
At night, the female pinworm crawls out of the anus to lay her itchy little eggs on the perianal folds, so you know that as soon as the sun set on La Cueva de los Muertos Chiquitos, everyone was either scratching or dealing with diarrhea.  It doesn’t sound like much of a party for them, but it does provide us with lots of information 1,300 years later!

As we continue collecting parasite data from this site, we will gain a picture of the daily lives of people who left no written record, only ancient nuggets of information reflecting what they ate and what was eating them.

Friday, July 3, 2015

Fast Times at the Annual Meeting of the American Society of Parasitologists

Greetings fellow parasitophiliacs! First of all, let me begin how I've begun far to many of my most recent posts by apologizing for my lack of writing lately. As a PhD candidate, I could come up with a million excuses...namely that I'm focusing heavily on my dissertation at the moment...but suffice it to say that I've had good intentions without the available time it takes to write something that you *hopefully* will enjoy reading.

I'll try to keep today's post short and sweet without getting too sentimental. Last weekend I attended my first American Society of Parasitologists meeting. I've been a member of this society for several years, but this was the first time I was able to go to one of the annual meetings.

This meeting was held over the course of four days in Omaha, Nebraska. The meeting consisted of a wonderful mix of student and faculty presentations covering a wide range of parasitological topics. There were a few symposia on topics that included undergraduate education and community outreach with regard to parasitology. These symposia featured several excellent talks by prominent members of the society.

For me, the most fun part of the meeting was the ability to catch up with other parasitologists and to have the chance to meet some of the "big names" for the first time. Like any young professional, I always leave wondering if I made the good impression that I hoped to make or if I said something stupid without realizing it. However, everyone that I met was welcoming and kind, so if I did say something stupid, they were nice enough not to make me feel dumb. It's pretty amazing to be a part of a society that is full of so many people who make you feel like you belong even if they've just met you.

The president of the society described our gathering as being similar to a "family reunion". It certainly felt that way to me, even being a relative new-comer with regard to attending the national meetings. I got to see many familiar faces from the Southwestern Association of Parasitologists (SWAP) and Rocky Mountain Conference of Parasitologists (RMCP) meetings that I've been attending since Dr. Duszynski took me to my first SWAP meeting while I was working on my master's. It's always great catching up and seeing what sorts of things people are working on.

I was also fortunate to meet a number of new people, including fellow students and prominent parasitologists conducting research in all kinds of neat areas. I met the now past-president of the society, Dr. David Lindsay, and got to talk to him about Toxoplasma gondii and other fun coccidia that he has spent his career studying. He introduced me to his student, Richard, who is studying Sarcocystis. He also offered me some of his spit to help with my dissertation...I've never been so excited to have received such an offer! (He is seropositive for T. gondii, so I could really use his spit to help with some of my experimental work.)

I briefly met our new president, Dr. Mark Siddall. Dr. Siddall studies leeches and works at the American Museum of Natural History. We didn't talk long, but we did get to talk a bit about outreach for the society. I can't commit to much, but it would be good to give back to the society in some way. I plan to send him an email later to touch base about how I can help. (I'm thinking I'll pitch the idea of getting ASP on Imgur, which would be pretty cool!) He also talked to me a bit about my dissertation and offered to put me in touch with some ancient DNA people if I have time to add that component into my dissertation work. Additionally, I got to meet one of his students briefly. The student was doing this really great work with microCT scanning of leeches. The animations in his presentation were excellent.

I was able to meet with several people who took the time to speak with me about my dissertation work. First, I met Dr. Charles Faulkner. I have read several of Dr. Faulkner's papers, so it was very exciting to meet him in person. We had a couple of opportunities to chat about the molecular work that I will be embarking upon this August and he was kind enough to give me his thoughts on some of the parasite eggs that I've been finding in my samples. What a great guy!

I also met with Dr. Agustin Jimenez. I've known Agustin for several years and I was happy that he had time to chat with me at ASP. He sat with me for a good while giving his thoughts on some of my photos of parasite eggs from my material and he had lots of insights to share since he had published on material from the same site. He even sent me some supplementary material from his work on the site that I've been looking through since I got back to the station for the summer.

I got to talk with lots of other people, but this post is already starting to look a bit long, so I'll cut it short for now. Overall, this was a great meeting! I enjoyed the food, fun, and familiar faces that filled the venue and it was wonderful to meet so many fellow parasitophiliacs in one place. I look forward to next year's meeting and to doing a little bit of service for such an open and supportive society run by awesome people. :)

The Moral of the Story
If you love what you do, you should seek out societies of like-minded people. Attending these meetings is a great way to enhance your knowledge base of the discipline and to expand your network of colleagues (and friends if you are lucky). These gatherings open the door for collaborative efforts and can be hugely beneficial for troubleshooting your own research. Plus, a hotel full of parasitologists is a pretty fun place to be! Where else can you talk about parasites while eating and not have one person make a comment about how it's not appropriate dinner conversation? (The struggle is real!)

Tuesday, February 10, 2015

Spittin' ELISAs: Using Saliva to Detect Parasitic Infections

Over the weekend I attended a League of Legends tournament with my wonderful husband. Despite anticipating losing a day's worth of work, I wound up hanging out with another fellow parasitophile and then I got an e-mail from my advisor with a paper that I hadn't read yet. So, there I was, reading about detecting Trypanosoma cruzi via ELISA from salivary samples of modern people (well, people from 1995 anyway...). The paper's intro cited one study I was familiar with and FIVE that I wasn't. From that point on, I knew I'd be (eagerly and enthusiastically) reading a lot more over the weekend.

So this is a post for me for you. This is me reminding myself of what I learned and sharing it with you, which I suppose has been the goal of this blog all along.  I guess it just seems more overt at the moment.

Before we jump too far ahead, let's start by talking about what ELISAs are. ELISA stands for "enzyme-linked immunosorbent assay". It's a fancy phrase, but don't let it scare you too much; the concept is fairly straightforward. Essentially, when you are infected with a parasite, the parasite produces antigens that are specific to whichever parasite is infecting you. In response, your body produces antibodies that are specifically designed to deal with the infection of that parasite. ELISAs are tests that are designed to detect either the parasite antigen or the antibody produced in response to said antigen.

Each ELISA kit is parasite-specific to some degree or another. This is really dependent on the parasite. Some kits can detect antigens/antibodies produced by/in response to a particular species, while others can only detect parasites at the genus level, so you may not know exactly which parasite you have. In the medical world, this is sort of "good enough for government work" as you can often treat infections with species belonging to the same genus in the same manner effectively. (If you have a parasite that is susceptible to a the same treatment protocols as a different parasite, it doesn't really matter what you are treating for as long as the treatment works.) As parasite ELISAs are most often used in medical and veterinary settings for rapid diagnosis, the specificity is less of an issue. However, in the case of parasitological research, we have to be careful when we use ELISAs to assess parasitism. We have to pick the kits carefully and be aware of potential cross-reactivatity.

Parasite ELISAs typically work with two types of material: blood and feces. (Wooo-hoo!) As you might imagine, intestinal parasites are typically detected from feces while non-intestinal types of parasites are found via blood serum. The problem with serum is that acquiring it is invasive (and for those of us that study archaeoparasitology, not available for use). Interestingly, your body carries antigens and produces antibodies that wind up in places other than serum...say for example, in your saliva. Really brilliant people in the late 1980s and early 1990s figured out that you could detect a number of pathogens via ELISA testing using patient saliva rather than serum. The Chagas' paper I mentioned earlier cited three studies that found viral infections, two that demonstrated parasitic infections, and one that detected bacterial infections. The two parasitic infections were chronic schistosomiasis (Garcia and colleagues, 1995) and acute toxoplasmosis (Hajeer and colleagues, 1994). Plus the paper on Chagas', of course.

It seems that that literature grows silent on this topic after the 1990s. It doesn't seem that people found evidence that these previous studies were incorrect (as far as I can tell), so I'm wondering if it just fell off of people's radar or if it just became so well-accepted that people stopped writing about it. It's hard to say one way or the other from my limited knowledge of the parasite ELISA literature, but I'm excited to have found something that leads to more. (Before Saturday, only knew about the Hajeer paper, so now I have a little bit more to build off of, which is super exciting for me!)

The Moral of the Story
The point of all this is to tell those of you who, like me, knew/know very little about molecular work and its application to the field of parasitology. Testing saliva from people and animals is a quick, non-invasive way to do preliminary tests for certain types of parasites. It's amazing how far our technology has advanced and it will be interesting to see how these advancements help us to better understand parasitism in the world around us, past, present, and future. I'm hoping to find more parasite studies looking at the application of ELISA testing that utilizes saliva as the detection source, so this is also a request to keep your eyes and ears open and let me know if you know of work being done in the area. (Thanks in advance to those of you that actually do!)

Sunday, February 1, 2015

Sifting Through the Sediments: Parasite Eggs from Night Soil Contexts

While the last thing that most people would want to get in the mail is night soil, I'm one of those people who excitedly awaits for jars of this stuff to arrive. (Because one: Such material is super cool and because two: "most people" are boring.) In my last two posts, I discussed how we look for parasites in the context of mummified tissues and desiccated feces. Today, I'm going to introduce you to another great source of literal pay-dirt for archaeoparasitologists.

Night Soil Sediments from the Past
A nightman's calling card from the 1800s.
For those who haven't been introduced to the phrase "night soil", I'm referring to dirt that has human fecal components. The term originated from the olden days when people would shovel human waste out of cesspools and outhouses during the night and later usually sell the excrement to farmers as a fertilizer. Many of these people employed as "nightmen" or "night soil men" were not allowed to work during the day and made up a portion of the lowest of low classes in most places. This was early human waste management in Europe, Africa, and Asia long before modern standards of disposal.

As you've probably already figured out, there were lots of problems with sanitation in the past. Before modern indoor plumbing, people found a variety of ways to store their steaming piles of...stuff...before nightmen could come and haul it away. Some were indoor chambers for relieving oneself. This included things like chamber pots or water closets (the early ancestor to modern flushing toilets). Others were outdoor pit latrines such as the outhouse, the privy, the dunny, the biffy, or the long-drop.

As excrement, other waste materials, and soil fill these types of features, evidence of parasites is preserved in a stratigraphic way (with the oldest layers at the bottom and the youngest layers at the top). Archaeologist excavate these types of features along with middens (trash heaps), cisterns, and other collections of human waste from sites all over the world. These sediments are collected with provenience information carefully recorded and dates associated with other things recovered from the same layer.

Analyzing Latrine Sediments
Once these sediments make their way to people like me, they are examined using a sequential analysis model (or at least they should be) to gather all of the information that can possibly come from such material. To process this type of material, first we treat sediments with hydrochloric acid to react with any microfossil-binding calcium carbonate that might be present. Next, we use distilled water to screen heavy sediments and separate macrofossils (big pieces of plants, minerals, bones, insect remains, etc.) from microfossils (parasite eggs, starch granules, pollen, etc.) using the swirl technique. The macrofossils are dried and examined via a stereoscopic microscope. The microfossils are examined via light microscopy and exposed to further processing as needed.

SEM of Lycopodium spores.
Depending on the nature of the samples, we may need to use dangerous chemicals like hydrofluoric acid (for dissolving silicates) or zinc bromide (for heavy density flotation). We are very careful when using such things as they can be harmful if precautions aren't taken to protect ourselves. For example, we wear eye protection all the time...especially when we use zinc bromide because it attacks the optic nerve if splashed in your eye and can blind you. We also have lots of special safety protocols when we work with hydrofluoric acid as it can stop your heart if enough gets on your skin and you aren't treated quickly. Rule #1: Never do it alone, just in case. I'll be using this acid later this week for some sediments from Iowa. There will be two other people in the working on mites, and one hanging around in case I have any problems.

We also treat sediments with Lycopodium spore tablets just like we treat coprolites and mummy intestines. By adding a known amount of these spores as markers, we are able to quantify our microfossils and make sense of their presence in our samples. We use a microfossil concentration formula to determine the number of microfossils per unit (weight or volume) of sediment.

Taphonomic Issues
Like other kinds of archaeological materials, we must always consider the state of preservation for our samples. The addition of chemicals to break down excrement is something to be aware of in samples from certain places and time periods. As I learned from a recent set of historic samples from Missouri, the microfossils found in cisterns are fewer in number and much more degraded than those found in privies from the same time period.

We also must consider how often the sediments were exposed to abiotic agents of change, like wind and water. A series of wetting and drying episodes can degrade things as hardy as sporopollenin-laden pine tree pollen grains over time, leaving no evidence of anything that was once there. Biotic agents, like coprophagus (poop-eating) fungi, bacteria, and animals, can also affect what we find in latrine sediments.

From Privies to Parasites
Without going into too much detail about the types of microfossils found in latrine sediments, I thought I'd let all of you parasitophiles see some of the groovy parasite eggs that have been found from these contexts.

Parasite eggs recovered
from cemetery sediments.

Unfertilized  egg of
Ascaris lumbricoides

Molecular techniques have also been used on sediments to search for evidence of parasites that don't leave visible traces of themselves. Enzyme-linked immunosorbent assays (ELISAs) have been applied to samples in order to detect a number of protozoan parasites such as Giardia sp., and Entamoeba histolytica. 

Example ELISA plate.
Yellow wells = positive samples.
The Moral of the Story
Like mummies and coprolites, sifting through latrine sediments elicits reactions of both disgust and amazement from those following your work. The data that can be gathered from such studies are immense in volume and intensity. I have conducted a number of contract archaeology jobs that involved the analysis of latrine sediments, so I can literally call these types of material "pay-dirt" from both a scientific and from an economic standpoint. It is sad that so few researchers understand the importance and potential of examining latrine sediments, but at the same time this allows those of us who do see the value in these studies to work without a lot of interference. As always, these kinds of studies provide the best means of understanding what past people were eating and what exactly were eating them.

Sunday, January 25, 2015

The Copious Little Coprolite: A Tale of Underrated Informants

As you may or may not already know, a great deal of my dissertation work focuses on the analysis of desiccated human feces (i.e. "coprolites"). These remains can come from archaeological sites such as caves and trash middens, or from direct human contexts such as mummified intestines or even burials in some special cases (e.g. Nivelles). Coprolites most often form in arid environments, preserving within them a vast amount of information about their depositors' diets, medicinal plant usage, and pathogens.  By analyzing these tiny cornucopias of data, we are able to learn not only what people were eating and what was eating them, but also to use these data to elucidate patterns of human behavior as our ancestors interacted with the world around them. Today, we are going to pay homage to something that doesn't often get the recognition that it deserves...the copious little coprolite.

A coprolite from Hinds Cave, Texas.
A Brief History of Coprolite Analysis
The word "coprolite" began as a descriptor of mineralized dinosaur feces used for the first time by a paleontologist named William Buckland in 1829. By the 1960s, the term had been applied to other fecal forms preserved via desiccation in addition to mineralization and was being used to describe fecal materials from archaeological contexts  in addition to paleontological contexts. There have been three distinct phases in this history of coprolite analysis stretching from 1829 up to the present.

The first phase (1829-1960) began with the birth of the term "coprolite". The value of human coprolites was not recognized until 1896, when a botanist named John William Harshberger suggested that looking at seeds in coprolites could reveal information about ancient diets. The early 1900s that followed Harshberger's suggestion saw researchers examining coprolites for other plant remains, like leaves and twigs, in addition to faunal remains, such as the tiny bones found in fecal deposits from a wide range of archaeological contexts. By the 1950s, people began looking more at the neat stuff in human coprolites. They started looking at hair and feathers as well as shell fragments and insect remains. Today, the study of "macrofossils" (macroscopic plant and animal tissues found in coprolites) is a crucial element of coprolite analysis.

Eventually, people began seeking smaller sources of evidence that today we call "microfossils" (things like pollen, starch granules, and our beloved parasite eggs). The first evidence of parasitism in the prehistoric New World came from whipworm (Trichuris trichiura) eggs found in an Incan mummy in 1954. This began the transition of coprolite analysis into the second phase (1960-1970). This phase saw the development of specialized techniques for examining microfossils and laid the foundations for later expansion.

The superstar researcher of the second phase was indisputably a man by the name of Eric Callen. Callen is known to many as the first true coprolite specialist. He completed three major analyses of coprolites recovered from New World archaeological sites and was working on a fourth when he died tragically in 1970. Despite being ridiculed by colleagues for his interest in coprolites (which were regarded as useless by researchers of that time), Callen persevered to become a legend in a now much more respected field. He developed methods for rehydration (a crucial first step in analyzing coprolites) and standardized other techniques for evaluating fecal deposits.

Various pollen grains
A wealth of other researchers also worked on coprolites during this second phase. It was during this era that pollen analysis was integrated into coprolite analysis. These early studies yielded incredible insights into the diets, medicinal plant usage, and even seasonal site occupations of prehistoric peoples of the New World. This era also saw the flickering of parasite studies that would ignite the third phase.

The current phase of coprolite analysis began in 1970. This phase has been characterized by both refined methods of analysis and by the expanse of these analyses into more interdisciplinary realms. Coprolite analysis grew to be applied in a broader sense to archaeological questions beyond the direct discoveries of dietary remains and evidence of diseases in antiquity. Techniques for quantifying macrofossils were developed over the course of a decade. Macrofossil identification techniques were also becoming more sophisticated and researchers began comparing coprolite data from various archaeological sites to one another. Pollen analyses also became more refined as methods for quantification and interpretation were tested and standardized. The study of phytoliths, fungal spores, and starch granules also became integrated into coprolite analysis. This allowed for more rigorous and fruitful assessments of nutrition through time and space.
A variety of phytoliths from the Tangue site in China.
{A–c = rice bulliform; d–g = rice double peaked; h, i = phytoliths from broomcorn millet husk;
j = long saddle; k = scutiform-bulliform from reed; l = common bulliform; m = Cyperus type;
n = trapeziform sinuate (tooth type); o = woody phytolith}
Which brings us up to the birth and subsequent growth of the field of archaeoparasitology. With foci in Brazil, Canada, Chile, England, Germany, Peru, and the United States, analyzing coprolites for evidence of parasitism grew exponentially. From the late 1970s right up through the early 1990s, methods for extracting and quantifying parasite eggs were developed. From the refinement of these methods came the ability of researchers to begin examining epidemiology of the past through the lens of parasitism. The following decades would usher in the integration of molecular techniques for finding evidence of parasitism that could not be seen with the naked eye. Studies using PCR and ELISA would revolutionize coprolite analyses to give researchers an even broader perspective of epidemiology in antiquity.

What's in a Coprolite and What Can They Teach Us?
As you likely gathered from the above, coprolites can treasure troves of taxonomic data. Breaking these into discrete components is how researchers conduct analysis, but only by re-combining dataset after discrete analyses are we able to get the full story that coprolites are trying to tell us. Reinhard and Bryant (1992) broke coprolites into their components in the following way:

1) Biological (Bacteria, Viruses, Fungi, Parasites, Insects, Pollen, Phytoliths, Macrobotanicals, and Macrofaunal Remains)

2) Mineral and Chemical (Sand, Grit, and Flakes, Charcot-Leyden Crystals, and Chemical Components)

All of these different elements that can be recovered from coprolites give dimension to the overall analysis. Taking in discrete datasets examining coprolites for a variety of components and synthesizing the information leads to the emergence of the bigger picture. By finding the eggs of fish tapeworms and tiny fish vertebrae in a land-locked population's coprolites, we can begin to understand prehistoric patterns of trade between this population an a coastal population. By finding the minuscule bones of rodents in the coprolites of cave dwellers, we can begin to picture the resource utilizations and ecological displacements that contributed to the origins of now-established zoonotic diseases among human populations today.

It is obvious, though not always intuitive for some, that diet and disease are intrinsically linked. This is true for the modern world as it was true for populations of the past. Understanding the nature of the diet-disease relationship comes to light by combining the data one can gather from coprolites. These little packets of poop are warehouses of information for understanding such relationships. They not only provide direct evidence (e.g. parasite eggs or pollen grains) but also proxy evidence (e.g. neotropical parasites found in pre-clovis coprolites from the pacific northwest point towards coastal human migration patterns into the new world).

Coprolite analysis is a vital aspect of archaeoparasitology, but also reaches far into other disciplines. Such studies are important for dietary reconstructions, understanding the interactions of people and their environments, and inferring aspects of early human behaviors. Advances in the areas of medicine, food technology, and environmental adaptation can be reflected by the composition of macrofossils and microfossils present in coprolites.

Today, coprolite analyses are being used to examine the origins of many diseases that plague modern societies. Diseases as different in their etiologies as Chagas' disease (caused by a parasitic protozoan) and diabetes (a metabolic disorder). Tracing the origins of such diseases is no small or simple task, but can be done through the analysis of the copious little coprolites that await researchers interesting in unveiling their stories.

The Moral of the Story
I could go on with a long, eloquent speech doting on the awesomeness of coprolite analysis and droning on about how excited I am about my own dissertation work with these remains, but I think by now you've probably read enough to wet your appetite for exploring coprolite analyses on your own. (Or, at least I hope I've so piqued your interest.) Instead, I will leave you with a somewhat crude, but appropriate message: Don't let anyone give you sh*t for liking coprolites. Seriously, people are quick to put down great work that originates from looking at things that some deem as "gross". (This is typically due to their own ignorance as to the significance of said work.) As a parasitophile, you are probably no stranger to the disgusted reactions of people who don't understand the value of parasitiology. But we don't do it for them, now do we? We do it for us. We do it to better understand the intricacies of the world around us. We do it because our passion knows no bounds. As a coffee cup that sits in an unnamed parasitology lab states: Don't let the bastards get you down!

Sunday, January 18, 2015

Show Me the Mummy!: A Journey into the World of Mummy Studies

This week I embarked upon my first collaborations with an amazing person that I met my very first semester here. She was an undergraduate back in those days, but she has since grown into working on a graduate degree through a dental program and...oh yeah, she's a Fulbright scholar. ;) She spent a year in Chile examining the hair (which, apparently wasn't always attached to the head) of mummies. I am honored to be joining the effort to get a few papers out from the data that she collected before she made her way back here for dental school. Until these data are published, I can't really say too much about what we are doing, but meeting with her earlier this week got me to thinking that I should do a blogpost on mummy studies.

So here I am...finally getting back into that series that I wanted to start back in October, when things got crazy. I hope y'all enjoy this journey into the exciting and totally underrated world of mummy studies.

Mummies Across Time and Space
Xin Zhui, a.k.a. "The Diva Mummy"
As soon as you read the word "mummy", I'm sure your first thought was "EGYPT!"...or at least that word was in whatever your first thought was. Yes, there are some awesome mummies in Egypt and those are the mummies that have garnered the post popularity in global media. However, there are LOTS of other places in the world that can boast of their own mummies. There are mummies in Asia...that's right, Japan, Korea, Mongolia, China all have mummies. In fact, one of the most well-preserved mummies ever discovered was the body of a noble woman named Xin Zhui who died in 163 BCE. She lived a lavish lifestyle, but died of a heart attack around the age of 50. The care taken to preserve her body along with all of the artifacts found over 2,000 years after she was entombed have earned her the nickname "The Diva Mummy". Her body was so perfectly preserved that when researchers examined the body, they commented that it was almost like doing an autopsy of a recently deceased person. Her limbs were flexible and her organs were remarkably in-tact. Mummy researchers learned a lot about the health of this person, including that she harbored tapeworms! (Yay parasites!)

Mummies have also been found in other parts of the world like Europe and South America. I've done a little bit of work with European mummies (from Lithuania and from Italy) that were much younger (1700s and forward) than the Egyptian mummies or most of the mummies from Asia. The previously mentioned work with the Chilean mummies will be the first work I'll have ever done with South American mummies. The Chinchorro mummies, found in present day Chile and Peru, are the oldest artificially mummified human remains in the world. You heard that right. The oldest of these mummies predates the oldest Egyptian mummies by about 4,000 years!

Now, I could easily spend hours talking to you about the differences in mummies across the world because they are just so diverse and fascinating, but this is a blog post...despite my propensity to sometimes get a little long-winded. Suffice it to say that mummies can (and are) found in a variety of places on this planet and that they range in age from around 7,000 BC to much more modern mummies who died in say, the early 1900s (AD).

Types of Mummies
There are several ways that would could split up mummies by "type", but I'm just going to break it into two broad categories for today's purposes. First, you could have a "prepared", "artificial", or "anthropogenic" mummy. These terms all refer to bodies that did not undergo natural mummification as a product of the corpse's depositional environment. These mummies were instead created by intentional preparation of the bodies. Most people think of these kinds of mummies when they picture mummies. Long before embalming, mummification was common practice for dealing with the remains of the deceased in certain parts of the world. Most people think of Egypt, with their whole wrapping, organs in jars, and pulling the brain out through the nose things, but the way that various cultures prepared mummies are as unique as the cultures themselves. Often times, the bodies were eviscerated and packed with plant material like straw to help maintain the shape of the now hollowed out body. There were frequently local (or sometimes imported) oils, vinegars, and herbs used on the bodies. Bodies were typically tightly wrapped in linen or other textiles and placed in a well-ventilated area to allow for drying. Some bodies were later placed into coffins, sarcophagi, or even glass viewing cases.

Ötzi the Iceman
However, there's more than one way to make a mummy. Some of the most famous mummies in the world are the bodies of people who were mummified unintentionally as a product of the environment in which they died. These of most frequently referred to as "spontaneous" mummies. Arid environments are particularly good for naturally drying out the body. Thus we have some excellent mummies found in desert regions, like the Chinchorro mummies found in South America's Atacama desert that I mentioned earlier. Mummies can also be found in arid environments that are cold, like the mummy known famously as Ötzi the Iceman. This mummy was discovered by some Germans hiking in the Alps. The hikers thought they had stumbled upon the body of another hiker who had had an accident, but it turns out that the body was 5,000 years old. Political issues arose when Italy and Austria both tried to claim the body, but in the end it was determined to have been on Italian soil.

Head of the Tollund Man
Bodies can also be preserved by the environments peat bogs. When a person's body is left in a peat bog, the bones tend to dissolve because of the acidity of the bog itself (remember that bones have lots of calcium phosphate, which is basic in nature). However, the acidity of bogs along with having little to no oxygen, and lower ambient temperatures creates an amazing preservation environment for human skin. The skin preserves extremely well, though it does get crazy dark in color making them appear almost like statues in the photographs that I've seen. These conditions include highly acidic water, low temperature, and a lack of oxygen, and combine to preserve but severely tan their skin. While the skin is well-preserved, the bones are generally not, due to the acid in the peat having dissolved the calcium phosphate of bone. The Tollund Man is one of the most famous bog bodies, belonging to a man who was hanged sometime between 375-210 BCE.

As a fun side note, mummies don't have to be humans. (But you've probably heard of how the Egyptians mummified cats...because you're a smart one!) Egyptians also mummified dogs...and lots of them. I read a neat study a while back that looked at the ectoparasites on Egyptian dog mummies. I did a post about it, and later a presentation at a parasite seminar. (You can read it here, but please keep in mind that I wrote it a few years ago and I've learned a lot more about taphonomy and parasitology since then.) Egyptians also commonly mummified pet monkeys, gazelles, mongooses, and a variety of birds. Aside from pets, Egyptians mummified other animals, including crocodiles, baboons, fish, snakes, and even bulls, for religious purposes. I haven't really heard of any other cultures that mummified animals, but I wouldn't be the least bit surprised if such cultures existed.

Mummy Studies
The field of mummy studies is an ever-growing one. As we become more technologically advanced, we are given the opportunity to really examine mummies to help us answer questions about life in the past. Mummy studies give us insights into the worlds of people who lived long ago. By analyzing mummies, we are able to understand when these people died and often times under what circumstances. We learn about their diets, medical practices, and funerary rituals. We learn about their societies and are able to tell their long-since forgotten stories.

Mummy studies brings together researchers from all kinds of educational backgrounds. The expertise of archaeologists, anthropologists, radiologists, epidemiologists, forensic scientists, palynologists, medical historians, and, of course, archaeoparasitologists, are brought together to put together the stories of these mummies. The patterns of culture, diet, and disease begin to emerge as mummies reveal their secrets to these researchers.

If any of you are interested in mummy studies, I'd like to inform you of a mummy field school that is currently in the making to begin in the summer of 2016. The course will consist of 15 days in Italy studying the mummies of the region. You'll actually get to do hands-on analyses of some of these mummies as class projects after you learn from experts all about how such analyses are conducted! There's even a possibility that yours truly will be there as either faculty or staff...but let's not get too far ahead of ourselves! (Dissertation OP.)

Mummies and Archaeoparasitology
Many of you may have gotten this far asking the question, "So, when do we get to learn more about parasites?!?!" Okay, okay...let's get to the parasites! Like other areas of mummy studies, the recovery of parasite data is largely dependent on the preservation environment and on the available technology of the people studying mummy parasitism. The analysis of mummified remains can (and has) revealed evidence of ectoparasites (as you already know from talking about the ticks and hippoboscids found on the mummies of dogs from Egypt), helminths (i.e. "worms"), and even protozoans. Yes, there's a little something for every kind of parasitophiliac when it comes to mummy studies!

Lice from a pre-columbian, Chilean mummy.
Click here for a link to the paper.
One of the coolest things about ectoparasites is that they tend to preserve well since we are typically referring to arthropods like ticks, fleas, and lice when we use the term "ectoparasite". In terms of human mummies, lice are the paydirt of ectoparasite-related archaeoparasitology. Lice can not only be found in their adult states on mummies, but also exist in the form of nits and nymphs. For those who don't know, "nits" are cases that house developing lice and are cemented onto the shafts of hair in an infested person. These nits, both with and without nymphs inside of them, can be found on the hairs of mummies. Counting the number of these nits on a small section of hair can allow for quantified comparative data across various analyses of head lice and their mummified hosts. Currently, I'm involved in the preparation of a paper or two that will look at the lice of mummies from the Atacama desert of South America. I'll be sure to post all about it when this paper (or papers) is (are) published. Be on the lookout! ;)

Stole this one from my major professor's Facebook page.
It's an adult louse from a South American mummy!
Most of the studies published with regard to archaeoparasitology of mummies focus on the discovery of parasitic helminths. In fact, the first archaeoparasitological study ever published (Ruffer in 1910) described the discovery of calcified Schistosoma sp. eggs in the kidneys of two 12th dynasty Egyptian mummies. Since those days, mummies from around the world have  revealed evidence of infections with roundworms (Ascaris lumbricoides, Strongyloides stercoralis, Trichostrongylus sp., Trichuris trichiura, etc.), tapeworms (most often Taenia sp.), and flukes (Clonorchis sinensisDicrocoelium dendriticum, Gymnophalloides seoi, Metagonimus yokogawai, Schistosoma sp., etc.).

Paragonimus westermani eggs from
the liver of a female, Korean mummy.
Click here for a link to the paper.
My personal experience with mummies is limited, but growing with every passing semester. I've seen Ascaris lumbricoides and Trichuris trichiura eggs in a mummy from Lithuania and Clonorchis sinensis eggs from a Korean mummy. I've also analyzed mummies from other places and not found any parasite eggs. I'm hoping to expand this in the future as I become more involved with mummy studies.

Another aspect of studying mummy parasites is to look for things that can't actually be seen with our human eyes. I'm talking of course about protozoan parasites (one of my favorite groups of parasitic organisms!). Because these are delicate, single-celled organisms, they don't preserve in the way that helminth eggs preserve. Instead of leaving behind a physical form that can be found with the aid of a microscope, these parasites leave behind molecular traces that can be detected with the use of serological test kits, such as enzyme-linked immunosorbent assays (ELISA), or through the use of DNA detection techniques, such as polymerase chain reaction (PCR). These techniques have been most frequently utilized to identify parasites in archaeological materials such as coprolites and latrine sediments, but they have also been applied to mummy studies. For example, researchers have revealed that ancient peoples were infected with malaria (caused by Plasmodium sp.) by analyzing bone, muscles, and skin.

The conclusion of this section brings us back to the infinite awesomeness that will be the mummy field school mentioned earlier. Students will be working on independent research projects with the mummies. Some of those students will be looking specifically at the parasites that infected these individuals in life. It will be fascinating to see what new information will come from the systematic examination of these individuals over time.

The Moral of the Story
The world of mummy studies is a complex, interdisciplinary area with lots of discoveries just waiting to emerge from hard work of enthusiastic researchers. What we can learn from the past through archaeological material is always a puzzle, but mummies give us the unique ability to equate data with a particular individual rather than guessing at how many people are represented by a group of coprolites or a gram of latrine sediments. Understanding the diets, medical advancements, seasonality of death, and of course the diseases of mummies allows us to paint an epidemiological picture of past societies one person at a time. As I grow to be a more competent archaeoparasitologist, I can only hope that my path will cross with more and more of these astoundingly interesting individuals and the parasites that they hold on or within them.