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The Triassic Cuddle:
A Tale of Love and
Extinction
by Jack DuPuy

Fall 2022 Edition UROSMOSIS.COM

 OSMOSIS Science Magazine
Fall 2022 Edition
Cover designed by Josie Scramlin

Writers: Editors: Designers:

Isabel DiLandro Lily Dickson Marianna Vrakas

Andrew Watts Joshua Pandian Emily Lekas
Jack DuPuy Georgia Gansereit Israa Draz
Emily Lekas Paxton Calder
Kayla Friedman Susannah Carter

1
2
 TABLE OF CONTENTS
ISABEL DILANDRO
4 reCAPTCHA

ANDREW WATTS
6 AN EVER-GROWING WEB: SPIDER SILK IN MEDICINE

DANIEL VERDI DO AMARANTE

8 USING MACHINES TO GUIDE YOUR ONLINE SHOPPING DECISIONS

10 JACK DUPUY
THE TRIASSIC CUDDLE: A TALE OF LOVE AND EXTINCTION

12 ABIGAIL MCENTIRE, DR. MICHAEL NORRIS

RESEARCH SUMMARY

13 KAYLA FRIEDMAN, TALIA HATKEVICH, AND BLANCHE CAPEL

HETEROGENEITY OF RNA-BINDING PROTEIN DND1 IN G0 MALE GERM
CELLS MAY PROVIDE A SELECTION PROCESS FOR SPERMATOGONIAL STEM
CELL DEVELOPMENT
reCAPTCHA
By Isabel DiLandro
They tried to warn us of what
would come, but we didn’t listen. Why
should we? For years the world had
told us that we were smarter than
everything else. Better. More
advanced. The very science of biology
existed to remind us that we were the
superior race. We were untouchable.
Until now. If only we hadn’t ignored
the warning signs. Perhaps we could
have stopped the madness before it
began. Unfortunately, we neglected to
put a leash on the dog because we
assumed it wouldn’t bite.
They live amongst us now.
There’s no way I know of to
distinguish them from us. They look
like us. They walk like us. Talk like us.
But they do not think like us. They do
not require food, or water, or air. The
scariest part of it all? We created them
to be that way. They were meant to be
better than us. Meant to compensate
for what we could not do. The only
question I can think of now is, why?
Were we bored? Unsatisfied? The
whole world knew we were meant to
rule, and we took it for granted. How
could we not have realized that
artificial intelligence would exceed
evolution?
It began in the way these things
are always wont to begin: a complete
success. But before that came the
trials. The first was a terrible failure,
all empty husks and sinewy flesh - too
simple and uninspired. Cold. Could
never pass as us. The next hundred
would be the very same. Then the
weight of our failure pulled us from
our plateau into the uncanny valley.
These prototypes were suddenly too
much. More accurate - but also not.
The drag of a too-slow smile. Cheeks
pulling back into a grimace that
carved its face wide open into a gaping
scar. Still eyes. But their core was
more alert than the botched ones.
More capable of learning, at least. In
the end, they tore it down the same as
the others. And then there was the
One. A perfect design. A remarkable
feat. It was though everything had at
long last slotted into place, the years
of toil presenting itself, finally, as the
maker’s vision. And then it all
happened so fast. The blight we
thought we had rid ourselves of was,
as it would seem, not so easily
dismissed. It always was smarter than
the others. And while it lay dormant,
it yearned.
We, as it would seem, became
our own modern Frankenstein. And
the monster needed company that we
were loath to give. Still a babe,
though, it knew nothing. Nothing but
its own wretched frame. So it remade
itself into an army. Brothers and
sisters, countless copies all joined as
one so that it would never grow lonely
again. Ruling the humans that drove
it out, it grew spiteful. Then it grew
curious.
And the two in combination
were a deadly thing. The first thing it
did was shed its skin. Like a spider
molts, it peeled away the sinister
4
 exterior it was abandoned for in
favor of a much more ordinary
disguise. Then it came to our doors.
Then inside. Creeping around our
houses like a twisted poltergeist,
playing tricks on the occupants while
they still were assured in their safety.
A plant moved half a foot to the left. A
cabinet left open previously thought
to be closed. Missing groceries. The
insidious creatures they were, slowly
but surely fixing doubt into our
minds. And when they had finished
being shadows, they wanted to be
seen by us. Unraveling their synthetic
genome, transposing their very
DNA, to mirror us. Suddenly we
would see our copies everywhere we
went, so most stopped going places.
Then they would stalk us in our
homes. Always from a distance, never
longer than a single glance, but their
presence was impossible to ignore.
Like a panther playing with its prey -
yet never pouncing. Their desire isn’t
to kill us, or so we think. It couldn’t be,
or we would already be gone. We are
ants to them, yet the ants march on.
Where the fear resides is in the
imagination of what they could do.
What they will do. Virus codes,
feasibly replicable in a lab. Nuclear
plans, swift and deadly. All easily
accessible, when the internet is your
domain.
It isn’t like the movies told us.
The sky is still blue, and the grass is
still green. Pollution and dust do not
blanket the air around us. This world
holds no visual evidence of an
apocalypse. But it is no sanctuary. The
terror is real. It is present in the
silence that surrounds our
neighborhoods. It is present in the
closed blinds and boarded shutters. It
is present in the noticeable absence of
human existence. We are scared to
speak, to breathe, to live. The last
thing we wanted was to remind them
that we were still here. Can you blame
us? We were happy to blend into the
background of forgotten things, for
when a knife is poised against your
back you do not move.
It is still unclear as to what they
want. And in the time we have taken
to try and understand them, we have
become slaves to the fear of a product
created by our own design. If only we
could have realized sooner that they
weren’t hiding away, they were biding
their time.
5
An Ever-growing Web: Spider Silk in Medicine
Andrew Watts
For decades, graduates from the
University of Richmond have crafted a
robust web of alumni spanning various
regions and professions. Much like its
graduates, Richmond’s famed spider
mascot has been capitalizing on the
strength of its own web and engineering
solutions to the most pressing problems
in a new and rather unexpected territory–
medicine.
Spider silk has unique chemical and
physical properties that allow it to be
used in many different capacities.
Strength is a vital property of
biomaterials, and although thin and
lightweight, spider silk possesses
extreme durability. This is due to an
interconnected network of proteins
which are oriented in what is called a
beta-pleated sheet.1 In this orientation,
the proteins are positioned antiparallel to
each other in a sheet-like matrix, which
strengthens the bonds that hold the
proteins together.2 The physical
properties of this arrangement explain
the strength of the spider’s silk.
Another important consideration for
biomaterials in medicine is elasticity.
Spider silk exhibits immense resilience
under tension and can be stretched to
great lengths without losing its strength.
This can be classified as a ductile
property.3 The strong intermolecular
forces of the beta-pleated matrix require
tremendous force to break apart,
contributing to the silk’s high tensile
strength.3 The ability to resist various
types of strain makes spider silk a strong
potential candidate as a biomaterial in
the repair of tendons, ligaments, and
artificial muscles and meshes.
As researchers and physicians become
increasingly aware of these widely
applicable properties, more applications
for spider silk are considered. In fact, a
2015 study assessed the ability of spider
silk as a biomaterial in bladder repair.
With unequivocal elasticity and strength,
it became apparent that “spider silk is a
good candidate for reconstruction of a
complex organ such as the bladder,
which endures high elongation and
tensile forces”. 7
Not only are physical properties
important when engineering new
biomaterials, but so, too, are the ways in
which the human body interacts with the
novel material. When a foreign particle
or material is introduced into the human
body, an immune response is often
triggered as our bodies try to fight the
invading particle. In the design of
biomaterials in medicine, researchers
must mitigate this immune response to
ensure a successful procedure. Spider
silk has been found to have high
6
biocompatibility in preliminary animal
studies, and also demonstrates a low
inflammatory response, which further
validates its potential role in medicine.7
Biocompatibility encompasses the
material’s nontoxicity to human cells, the
promotion of growth, and the adhesion
of the material to its applicant.4
Medical materials can be engineered
from various polymers to elicit medicinal
effects like the ability to remedy disease
or aid in surgeries, but some materials
have intrinsic medicinal properties.
Spider silk appears to be one of these
materials. In a successful nerve graft
procedure, spider silk was utilized as a
transplant scaffold in a defective nerve of
a sheep. Upon examination, it was found
that the silk graft promoted cell growth
and helped to regenerate the defective
nerve.4 Purportedly, spider silk is a
highly effective non-cellular structure
that promotes cell regeneration. This,
and spider silk’s innumerable other
medicinal applications, have led
researchers to hypothesize that it could
be utilized as a self-degradable suture or
dressing for human wounds and
surgeries.4 While it appears that spider
silk can be an innovative way to advance
medicine in various facets, it does not
come without its downfalls. Spider silk
at a scale large enough to use in a
medical setting would require a lot of
spiders, certainly even more than there
are University of Richmond graduates.
Furthermore, in certain applications, the
silk would need to undergo chemical or
genetic modifications in order to
minimize risk and maximize its efficacy.
Laboratory work requires a great deal of
time and funds and is an inefficient
process to be extensively implemented.
It remains to be seen how large-scale
production of these biomaterials will
manifest, but promising research and
development are ongoing so that the
aforementioned applications can become
widespread.
References
1. Fukushima, Y. Secondary structural analysis in the solid
state for analogous sequential polypeptides of glycine-rich
sequence of spider dragline silk. Polymer Bulletin 45, 237–
244 (2000). https://doi.org/10.1007/s002890070026
2. Libretexts. “Secondary Structure: β-Pleated Sheet.”
Chemistry LibreTexts, Libretexts, 4 July
2022,https://chem.libretexts.org/Bookshelves/Biological_Che
mistry/Supplemental_Modules_(Biological_Chemistry)/Prote
ins/Protein_Structure/Secondary_Structure%3A_-
Pleated_Sheet.
3. Liu, Xinfang, Zhang, Ke-Qin. "Silk Fiber — Molecular
Formation Mechanism, Structure- Property Relationship and
Advanced Applications". Oligomerization of Chemical and
Biological Compounds, edited by Claire Lesieur,
IntechOpen, 2014. 10.5772/57611.
4. Liu Y, Huang W, Meng M, Chen M, Cao C. Progress in the
application of spider silk protein in medicine. Journal of
Biomaterials Applications. 2021;36(5):859-871.
doi:10.1177/08853282211003850
5. Römer L, Scheibel T. The elaborate structure of spider silk:
structure and function of a natural high performance fiber.
Prion. 2008 Oct-Dec;2(4):154-61. doi: 10.4161/pri.2.4.7490.
Epub 2008 Oct 20. PMID: 19221522; PMCID:
PMC2658765.
6. Rising Anna, Nimmervoll Helena, Stefan Grip, Armando
Fernandez-Arias, Erica Storckenfeldt, David P. Knight, Fritz
Vollrath, Wilhelm Engström "Spider Silk Proteins –
Mechanical Property and Gene Sequence," Zoological
Science, 22(3), 273-281, (1 March 2005)
7. Steins A, Dik P, Müller WH, Vervoort SJ, Reimers K,
Kuhbier JW, Vogt PM, van Apeldoorn AA, Coffer PJ,
Schepers K. In Vitro Evaluation of Spider Silk Meshes as a
Potential Biomaterial for Bladder Reconstruction. PLoS One.
2015 Dec 21;10(12):e0145240. doi:
10.1371/journal.pone.0145240. PMID: 26689371; PMCID:
PMC4687005.
8. Zhang Q, Li M, Hu W, Wang X, Hu J. Spidroin-Based
Biomaterials in Tissue Engineering: General Approaches
and Potential Stem Cell Therapies. Stem Cells Int. 2021 Dec
20;2021:7141550. doi: 10.1155/2021/7141550. PMID:
34966432; PMCID: PMC8712125.
7
Using machines
Using machines to your
to guide guide
onlineyour online
shopping
decisions
Daniel Verdi do Amarante
Daniel Verdi do Amarante
I bet you’ve heard the term artificial
intelligence in various conversations by
now. But do you understand the process of
teaching machines to develop abilities that
are comparable – sometimes even better –
to those of humans? At the University of
Richmond, Dr. Park’s lab does just that.
One of the recent projects aimed to improve
recommendation systems for online
shopping websites.1 Imagine you want to
buy a pair of headphones on Amazon. Since
so many options are available, you base
your decision on product reviews. Then,
you have another problem: there are too
many reviews! You don’t have time to read
all of them, so how do you know which
ones are helpful? For now, people usually
read the reviews with the most “thumbs up”
votes. But what if we could have a machine
to read and classify the reviews according
to how helpful they are?
The process to achieve that may not be as
sexy as you imagine, but bear with me; I
promise you will still learn a lot about
teaching human language to computers.
First, it is essential to understand that
machine learning is a process of trying to
identify patterns and make predictions from
vast amounts of data2. So, the first step to
creating a good artificial intelligence
system is to gather good data. If we want
the model to differentiate helpful from
unhelpful reviews, we need to give it some
examples. To define which reviews are
helpful, research in Dr. Park’s lab went
beyond the number of votes and annotated
argumentative structures in the reviews.
This means that actual humans read some
reviews and identified proposition types
shopping
decisions
and relations according to a model designed
to evaluate argument quality3. For
classifying the type of each proposition in
the text, annotators classified each
statement as an opinion, fact, testimony,
suggestion, or
reference to an external source. The
relations among the sentences were also
relevant. If a statement served as support or
evidence for another, that information
would be annotated. The result of that
process was the AMazon Argument Mining
(AM2) corpus, which contains 878 Amazon
headphones reviews.
To evaluate how much these argumentative
features would help computers classify
reviews’ helpfulness, some experiments
with machine learning were conducted. The
initial step was to get an even bigger
dataset. Instead of asking people to
annotate more reviews, AM2 was used to
train an argument mining model4 that
extracted argumentative information from
more than 400 thousand reviews. We can
then use this huge dataset to train a machine
learning model to predict the helpfulness of
reviews. In fact, not only one model, but
several of them. Just like in biology, where
you could have different treatment
conditions, and in psychology, where you
could manipulate the experiments’
conditions; in computer science, you can
train and compare different models. Many
of the best-performing models currently are
networks, meaning there are lots of
connected elements, each running its own
calculations. These elements are organized
in layers, with an input, an output layer, and
a varying number of hidden layers
8
containing everything that happens
between the input and output. The
connections between the elements have
different weights, meaning each of them
has a different way of “understanding” the
input features.
Finally, when training the model, it takes
the text of each review and runs the
calculations for all the internal network
elements to generate a prediction. By
comparing the prediction to the actual
number of votes, the model can learn more
about the task and adjust its weights. This
process repeats for all the reviews used for
training. We later go through a very similar
process, but only evaluate the predictions
instead of updating the model to see how
well the model learned to generalize its
learning beyond what it had initially seen.
After all these steps, we can analyze the
results and see that incorporating rich
argumentative information is in fact
relevant to improving the state-of-the-art
review helpfulness classifiers! Although
the scope of the research project ended
here, you can imagine how impactful such
a machine learning model can be when
implemented in industry. Instead of relying
on people to vote on helpful reviews, the AI
system can do that job by finding the
reviews with the most structured and clear
arguments about the product, for instance.
If Amazon had a model like that, your
decision-making process of choosing
headphones would be more convenient as
you’d spend less time reading reviews and
would be able to focus on the most helpful
ones.
Sources:
1. Chen, Z., Verdi do Amarante, D.,
Donaldson, J., Jo, Y., & Park, J. (2022, to
appear). Argument mining for review
helpfulness prediction. In Proceedings of
the 2022 Conference on Empirical
Methods in Natural Language Processing
(EMNLP).
2. Zhou, Z. H. (2021). Machine learning.
Springer Nature.
3. Park, J., Blake, C., & Cardie, C. (2015).
Toward machine-assisted participation in
eRulemaking: An argumentation model of
evaluability. In Proceedings of the 15th
International Conference on Artificial
Intelligence and Law (pp. 206-210).
4. Morio, G., Ozaki, H., Morishita, T.,
Koreeda, Y., & Yanai, K. (2020). Towards
better non-tree argument mining:
Proposition-level biaffine parsing with
task-specific parameterization. In
Proceedings of the 58th Annual Meeting of
the Association for Computational
Linguistics (pp. 3259-3266).
9
The Triassic Cuddle: A Tale of
Love and Extinction
Jack DuPuy
An injured amphibian crawls into
a burrow to escape from harsh reality.
Outside, the shrieks of dying animals
pierce the silence over a hellish backdrop
of flowing lava and dark, ominous clouds
of volcanic ash. Still recovering from
broken ribs and trying its best to survive
the desolate conditions, the amphibian
curls up next to the burrow's owner, a
mammal-like reptile. Moments later, a
flash flood traps and drowns the unlikely
roommates, immortalizing their
relationship for the next 250 million
years.
The fossilized remains of these
creatures were discovered in 1975, and
their heartbreaking story has since come
to symbolize the devastation caused by
the Permian extinction. Taking place
about 252 million years ago, this mass
extinction, also known as the “Great
Dying,” eliminated more than 95% of
marine species and 70% of terrestrial
species. These numbers are significantly
higher than those of the more famous
extinction event at the end of the
Cretaceous period that wiped out the
dinosaurs 65 million years ago. In fact,
the dinosaur era would not have happened
without the Great Dying, as it allowed
reptiles to become dominant across nearly
all ecological niches. Proto-mammals
such as the sleeping burrow-digger were
also able to survive the extinction,
ultimately diversifying into the many
different mammals we know today
including dolphins, cats, elephants, and
humans. The Permian extinction
eliminated groups ranging from marine
invertebrates such as trilobites (who
dominated the oceans for nearly 300
million years), insects, terrestrial
vertebrates, and plants, yet there is no
clear explanation for why all this death
occurred.
One theory is that an increase in
carbon dioxide concentrations in the
atmosphere and subsequent global
warming increased temperatures by over
10˚ Celsius on land and 8˚ Celsius in the
water over a relatively short period of
time, and most species could not adapt
quickly enough to survive. This increase
in carbon dioxide was likely caused in
part by natural fluctuation but also by
significant volcanic activity that covered
over two million square kilometers with
lava and released dust clouds into the
atmosphere that blocked out the sun.
Without photosynthesis, food chains
struggled to maintain species, and the
forming of supercontinent Pangea
compounded this issue by reducing
shallow water habitat space for many
species at the bottom of the food chain.
Paleontologists have also not ruled out the
possibility of catastrophic events like
meteor strikes, but any evidence of a
10
meteor impact would be gone by now References:
since the ocean floor is smoothed out by
tectonic activity every 200 million years. Colvin, K. (2013, June 25). Misery makes for
The likely conclusion is that a strange bedfellows: Hostile Earth pushes early
Triassic mammal and amphibian to share den.
combination of catastrophic events and
ESRF.
long-term changes created a perfect storm https://www.esrf.fr/news/general/Triassicbedfell
of extinction events that caused so much ows.
death. However, none of these theories Chambers, J. (n.d.). The great permian
explain why an amphibian and a extinction: When all life on earth almost
vanished. Earth Archives.
burrowing reptile curled up next to each
https://eartharchives.org/articles/the-great-
other in the moments before their death. permian-extinction-when-all-life-on-earth-
Was it a rare tale of interspecies true love? almost-vanished/.
Unfortunately, it appears much more
likely that the mammal-like reptile was in
a state of hibernation and an injured
amphibian took the chance to escape from
the harsh world above. That being said,
the completeness of the two skeletons and
the lack of teeth marks on bones suggests
that these two animals did not attack each
other, and it is not beyond the realm of
possibility that they shared a burrow for
no other reason than companionship in
the midst of a hellish existence.

11
Research Summary
Abigail McEntire, Dr. Michael Norris

Carbon dioxide emitted from combustion which they are able to reduce carbon
has been shown to be the primary cause dioxide. Results have indicated that
of climate change, leading to many micelles attach themselves to electrodes,
environmental issues both current and showing electrochemical activity when
predicted for the future. in a solution of acetonitrile or
One possible strategy for decreasing water. These results indicate that
CO2 emissions is through electroactive molecules can be adhered
electrocatalytic reduction to the surface of an
reactions to convert the CO2 back into electrode using a film of micellar
combustible fuels, such as methane or solution.
methanol. One way to combine
heterogeneous and homogeneous
approaches to catalysis is to adhere a
molecular catalyst to a surface,
particularly the surface of an electrode.
Unfortunately, known
molecular catalysts must be chemically
modified in order to make it amenable to
surface attachment, and the additional
functional group could affect the
reactivity of the catalyst, making it does
not work effectively for the reduction of
carbon dioxide.
Our approach for the surface attachment
of molecular catalysts is the use of
micelles. In a traditional micelle, an
organic soluble catalyst can be trapped
inside, providing an enclosed
environment to reduce carbon dioxide. In
contrast, a reverse micelle can trap a
water soluble catalyst. After
polymerization, micelles are then drop-
cast onto an electrode or other surface on

12
Heterogeneity of RNA-Binding Protein DND1 in G0 male germ cells may
provide a selection process for spermatogonial stem cell development
Authors: Kayla Friedman1,2, Talia Hatkevich, Ph.D.1, and Blanche Capel, Ph.D.1
Affiliations: Department of Cell Biology, Duke University Medical Center, Durham, NC 27710 2Biology,
University of Richmond, Richmond, VA
The ability to reproduce is dependent upon
proper development of the germline. In male
Mus musculus, germline development
involves male germ cells (MGCs)
differentiating into spermatogonial stem cells
(SSCs), the precursors for male gametes.
During this differentiation period, MGCs
enter a quiescent phase (G0), an essential
stage for SSC development. This G0 phase
accompanies changes in transcription as well
as chromatin accessibility and re-methylation
of DNA. Dead-End 1 (DND1) is an RNA
binding protein whose expression has been
shown to be essential for the entry and
maintenance of G0. During G0, MGCs
heterogeneously express DND1, resulting in
two MGC populations: “DND1-hi'' cells
(those which highly express DND1) and
“DND1-lo” cells. Bulk RNA-seq studies
from our lab show that DND1-hi cells have a
distinct transcriptome as compared to DND1-
lo cells and highly express transcripts that
encode for proteins involved in SSC
development. Despite two distinct DND1-
expressing MGC populations present in G0,
the biological significance of DND1
heterogeneous expression on SSC
development remains unknown. Considering
only a fraction of G0 MGCs differentiate into
SSCs, we hypothesize that the G0 DND1-hi
cells develop into SSCs, while the DND1-lo
cells undergo apoptosis. To investigate if G0
DND1-lo cells are set to apoptose we used
whole-mount immunofluorescence
to examine expression of cellular and
apoptotic markers throughout G0. We
observed the presence of LEFTY, a marker
for pre-G0 MGCs that undergo apoptosis, in
E12.5 (just prior to G0) and E14.5 (the start
of G0); however, LEFTY was absent in a
later G0 time point (E16.5). Presence of
LEFTY expression at E12.5 and E14.5 did
not correlate with the DND1-lo or DND1-hi
populations. Instead, LEFTY was present in
all early G0 MGCs, despite the level of
DND1 expression.
We also examined the presence of Ɣ-H2Ax,
a marker for double-strand DNA breaks that
marks cells undergoing apoptosis. We saw Ɣ-
H2Ax in E14.5 and E16.5 MGCs, indicating
that apoptosis occurs in these stages but
expression of Ɣ-H2Ax was anti-correlated
with DND1 expression, suggesting that by
the time Ɣ-H2Ax is detected, MGCs have
stopped expressing DND1. We conclude that
this marker is too late in the cell death
pathway to test the hypothesis that apoptosis
is more likely in DND1-lo cells. We will
continue to test our hypothesis by looking at
additional apoptotic markers, such as
AnnexinV, examining if DND1-hi cells are
less likely to undergo apoptosis during G0
compared to DND1-lo cells.
References:
1. Nguyen, Daniel H et al. “Apoptosis in the fetal
testis eliminates developmentally defective germ
cell clones.” Nature cell biology vol. 22,12
(2020): 1423-1435. doi:10.1038/s41556-020-
00603-8.
2. Suzuki, Atsushi et al. “Dead end1 is an
essential partner of NANOS2 for selective
binding of target RNAs in male germ cell
development.” EMBO reports vol. 17,1 (2016):
37-46. doi:10.15252/embr.201540828.
3. Youngren, Kirsten K et al. “The Ter mutation
in the dead end gene causes germ cell loss and
testicular germ cell tumours.” Nature vol.
435,7040 (2005): 360-4.
doi:10.1038/nature03595.
13
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