Summaries

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GENE479 SEMINAR SUMMARIES
1. PhD, Oğuzhan Beğik
Postdoctoral researcher Oğuzhan Beğik introduced us the topic called “Characterizing the
RNA modifications and polyadenylation landscape using nanopore sequencing”. His research
was generally based on RNA modifications. He divided their studies into three subclasses.
Firstly, they used RNA modification-related proteins (RMPs) for integrative analyses. Then,
other study was related with detecting RNA modification with direct-RNA sequencing. Last
one was capturing diverse transcriptome with Nano3P-seq. He started with their curiosity
about RNA that is a dynamic substance that goes through several changes. He mentioned
about RNA processing which is 5’capping, splicing, 3’end processing and polyA tailing, then
chemical RNA modifications contribute diversity and complexity. During presentation
provided by Oğuzhan Beğik, we learned about RNA modifications and their locations and
functions. They are reversible and happens nucleus or cytoplasm depends on which
mechanism is involved, mostly rRNAs. He talked about first task that is manual curation of
RMPs. He utilized an article “The N6-methyladenosine (m6A)-forming enzyme METTL3
controls myeloid differentiation of normal hematopoietic and leukemia cells” to explain
nucleotide modifications in mRNA and its consequences in treatment. Also, we learned that
duplications lead to change in target RNA, tissue-specifity, and modification type. Then, he
continued to RMPs that are dynamically expressed in during sperm formation. He
demonstrated this in scRNA-seq data table and immunohistochemistry of testis and
epididymis. We acquired knowledge about RNA modifications in cancer treatments and
RMPs are dysregulated in cancer and have prognostic effect in cancer patients. Moreover,
Oğuzhan Beğik mentioned about challenges and questions of RMPs. Secondly, he passed on
methods to map RNA mod. One is Antibody-based RIP-Seq which has antibody binding,
immunoprecipitation and library preparation steps. Other one is chemical-based Chem-Seq
which as chemical treatment, reverse transcription, and finally library preparation steps. RT-
signature based Mismatch or drop-off signature is another method to map RNA mod. There
are limitations to these methods. Limited antibody, chemical and low specifity of antibody
(can be very dangerous). In addition, short read leads to no isoform information. Over and
above that, nanopore sequencing is a new technology. It has better qualifications compared to
methods that are talked earlier. There is no PCR that is unbiased quantification and full-length
read. “A” methylation can be detected by nanopore. Most abundant RNA modification is m6A
and can be detected by nanopore seq. Distortion signal is not located at only one base,
neighboring of the modificated site is detected by nanopore. EpiNano measures mismatch
frequencies, base quality, deletions and detect also m6A modifications that causes some
errors. He lastly commented on rRNA especially rich in pseudourine and 2’-O-methylation
modifications guided by snoRNAs.
2. PhD, Ulaş Tezel
Postdoctoral researcher Ulaş Tezel addressed us the topic called “Quaternary Ammonium
Disinfectants”. Despite our inadequate understanding of quaternary disinfectants' effects on
the environment and human health, their usage has increased dramatically as a result of the
epidemic. Quaternary ammonium compounds (QACs), which are included in aerosols, wipes
and other disinfectants, have become a common exposure for people. But the effects of
increased QAC use led to its finding in human blood and breast milk. Ulaş Tezel and
associates looked into possible unidentified side effects using Pseudomonas sessilinigenes, a
bacteria that is skilled at breaking down QACs. Tetradecanoic acid, the breakdown product,
provides other environmental bacteria with a source of carbon. QxyA, also known as a Rieske
oxygenase, is the enzyme that breaks down QAC when oxygen is present. QxyR controls a
group of seven genes, including the QxyA gene. When QACs are not present, QxyR prevents
RNA polymerase from attaching to the promoter region, which impedes QxyA's translation.
Researchers are now examining if the QxyA gene is connected to the promoter region that
QxyR blocked. They are using the Pseudomonas sp. Biomig-1 strain in their tests, which is
capable of breaking down benzalkonium chlorides (BACs) and tertiary ammonia (BDMA) in
addition to QACs. Moreover, observations of certain transposon elements in the QxyA gene
indicate their potential role in activating the QxyA gene cluster.
3. PhD, Eva Katharina Engelhardt
Postdoctoral researcher Eva Katharina Engelhardt presented us the topic called “Change
of Biodiversity: Perspectives from Computer Models in the Past, Present, and Future”.
Natural ecosystems are subject to major changes as a result of human activities including
urbanization, climate change, and deforestation. Studies are using computer models that
examine the complex interaction between species and their environments more often in an
attempt to understand the impact of these changes on biodiversity. These models are useful
resources for monitoring organisms and tracing their evolutionary history. Through the
creation of graphs grounded in empirical evidence, scientists can get a deeper understanding
of the variables impacting the proliferation or decline of particular species within given
regions. These graphs are created by examining historical patterns and determining the factors
that contributed to them. Although these models make future predictions easier, there are
drawbacks. The majority of research focus on vertebrates, which narrows the range of species
that may be successfully tracked. The answer comes in the form of occupancy modeling,
which provides a way to pinpoint the location of a species and how its presence fluctuates
over time and space. Real data and observations form the basis of the occupancy modeling
process and are used to create graphs. By looking at these graphs, one may see how species
populations fluctuate over time a phenomenon known as a species trend. Researchers begin
focusing on examining the causes of these changes. Resources, climate change, interactions
with other species, and the ability of the species in question to disperse are some of the drivers
impacting these patterns. The quality of the occurrence and distribution data utilized as the
first input determines how accurate the forecasts are when using computer models to see into
potential future situations. The model's capacity to forecast the condition of ecosystems and
species dynamics in the future is strongly influenced by the selection of initial data.

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Büşra Boztepe

1. PhD, Oğuzhan Beğik

2. PhD, Ulaş Tezel

3. PhD, Eva Katharina Engelhardt

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