Journal Club: Sep 06

For this week's Journal Club meeting Helen posited "Organisms as ecosystem engineers" (Jones et al. 1994). This paper defined ecosystem engineering, which classifies ways that non-trophic interactions between a species and the resources in their environment affect other species in the environment as a whole. Jones and colleagues describe 5 cases considered ecosystem engineering, 2 autogenic (the organism's structural change affects a resource) and 3 allogenic (the organism modifies an aspect of the ecosystem that affects a resource). The classic examples being beaver dams altering waterways as 'case 4' allogenic engineers, and the formation of mussel beds affecting erosion of inland marshes as 'case 5' autogenic engineers. Though this paper brought to light considering ecosystem engineering as an important ecological effect, the 5-case classification system has not been canonized in the literature. More recent papers have strayed from the autogenic/allogenic classifications, such as Berke 2010, which instead breaks down ecosystem engineering into four categories: structural engineers, bioturbators, chemical engineers, and light engineers. 


Helen is beginning work towards a review paper exploring ecosystem engineering in the human microbiome. Specifically, focusing on microbial structural engineers (encompassing both autogenic and allogenic examples) by combining the frameworks described in the above two papers. Some examples discussed were biofilms, which modify O2 and nutrient concentration, as well as contribute to pH heterogeneity. Fungal highways are also another clear example of structural engineers, providing a water envelope around the fungal hyphae through which bacteria travel, although this phenomenon has not been described in the human microbiome. Dental caries erode teeth and provide new habitats for oral microbiota, and cervical mucus during pregnancy is affected by bacterial vaginosis leading to increased porosity of the mucus plug and a higher risk of premature birth. Candida albicans is an example of a microbe that forms biofilms and hyphae, on which S. aureus can bind, making it an autogenic structural engineer. 


The ecosystem engineering model, however, contains many grey areas and areas that do not easily translate from macro to micro biology, but the ubiquitous ability to apply ecosystem engineering provides an important framework through which to view interactions. One specific issue to overcome is the definition of a resource for microbes. For microbes a resource can come in many forms and is often concentration dependent. Another gray area is whether or not to consider immune response as ecosystem engineering, as it both affects the environment but could be further specified consider just inflammation as the engineer. 


Member Monday: Meet Sarah Ansari!

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Sarah is currently working on evolving better degraders of mycotoxins using the Rhodoccocus species. She is working with Marco with the ultimate goal of engineering a microbial bioremediator.

She is still exploring the extensive world of biology, but is most interested in biomedical research and has worked at Novartis on their cancer-curing drug, Kymriah in pre-clinical trials. She has also recently become interested in evolutionary biology, and its potential application to medicine. 

Outside of lab, you can find Sarah in the depths of O’Neill library, doing some form of homework, or binging on Brooklyn-99 or Arrested Development elsewhere.

In the future, Sarah would like to join an organization, such as Doctors without Borders, and practice in underdeveloped countries in an effort to eliminate the disparities in healthcare at a global level. 

Member Monday: Meet Ezdean Alkurdi!

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Ezdean, also known as Deno, is currently working with different methods of homologous recombination to edit the genome of E. coli. He is also transitioning into computational work.

He has a passion for genetic engineering partially because he gets to feel like he is building his own Frankenstein but instead of a zombie he can make cute Bacteria that glow.

Outside of lab, he loves hiking, biking, running, swimming and lifting! He also loves videogaming (League of Legends, Overwatch, Fortnite, PUBG, and Counter-Strike Global Offense).

His plans for the future are still largely undecided, but he is looking into MBA programs and is open to working in Consulting or banking for a couple of years. He eventually want to work for a Venture Capital firm (specialize in healthcare or technology).

Journal Club: November 5

This week, members of the Momeni Lab Journal Club discussed the paper “Candida albicans-Induced Epithelial Damage Mediates Translocation through Intestinal Barrier” by Allert and Forster. Allert and colleagues effectively determined the mechanism for how the fungal pathogen C. albicans, usually a harmless fungus colonizing human mucosae, translocates across the intestinal barrier to cause lethal bloodstream infections.


According to the paper, the authors conducted a screen of greater than 2,000 C. albicans deletion mutants to identify genes required for cellular damage and translocation across enterocytes. Analysis isolated the answer of how C.albicans is able to participate in transcellular translocation to hypha formation, barrier damage above a minimum threshold level, and decreased epithelial integrity. In vitro cell culture models concluded that translocation was correlated with the ability of the C. albicans to secrete candidalysin, a peptide toxin deriving from the hyphal protein Ece1. The cytolytic peptide toxin was found to be essential for damage of enterocytes and was proven to be a key factor in fungal translocation due to its ability to take advantage of a necrotic weakened epithelium. Overall, this suggests that transcellular translocation of C. albicans through intestinal layers is mediated by candidalysin.


This conclusion is important background information for research performed at the Momeni lab. Currently, we are conducting research looking at the spatial ecology of interactions between C. albicans and Staphylococcus aureus. More information about the paper discussed this week can be found here:


Member Monday: Meet Helen Kurkjian!


Helen’s current research focuses on the role of spatial networks in microbial ecology.  Habitat connectivity is important to the survival and growth of many populations, but its relevance to microbes is not as well understood. Presently, she has two main projects.  The first is looking at the spatial ecology of interactions between Candida albicans and Staphylococcus aureus.  The second project uses artificial landscapes called Metapopulation Microcosm Plates, which she invented as part of her dissertation work, to measure the effects of dispersal corridor spatial arrangement on microbial population growth.  

Broadly, Helen is interested in population and community ecology, especially questions that fall under the umbrella of "Why do organisms survive and thrive in some times and places but not others?"  She is focusing on the spatial ecology of microbes right now, but in the recent past, she has also worked with plants.  She did her master's work on the population ecology of a rare plant, the Lassics lupine, and how seed predation by small mammals affects its demographics.

Outside of lab, Helen likes to read, especially mysteries and science fiction, and she enjoys cooking (and eating) new dishes.  She tries to get out for walks when she can and she does a little bit of woodworking. She hopes to be here in the Momeni Lab for the next couple years. Then she hopes to find a faculty position at a small college.  

Member Monday: Meet Natalie Sandlin!

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Natalie is a first year graduate student in the Momeni Lab. She is interested in molecular microbiology and utilizing its tools and techniques to understand how microorganisms do specific functions. More specifically, her research interests include host-pathogen interactions and bioremediation.

Her current work in the lab involves a project involving the bioremediation of mycotoxins using bacterial species. The current focus is on artificial selection to evolve Rhodococcus species and understanding the factors contributing to their degradation ability, with the overarching goal being to evolve the strains into better degraders of mycotoxins.

Outside of the lab, she enjoys baking, reading, and playing card and board games. In addition, she also really enjoys traveling; her dream is to visit all the US National parks (16/60 visited so far) and visit Zimbabwe to see elephants in the wild (her favorite animal). The plans for the foreseeable future are to make it through grad school and get her PhD, and hopefully to go into industry and work as a research scientist after.

Member Monday: Meet Marco Zaccaria!


Marco’s current research is about the formalization of general principles to inform the engineering of a microbial bioremediator. At present, he is focusing on two projects aimed at mycotoxin biodegradation: 1) Artificial Selection of Rhodococcus sp.  2) Directed Enzyme Evolution of the enzyme Laccase by Trametes versicolor.

His main interest is Evolutionary Biology, especially in the context of bioremediation oriented Synthetic Ecology. Moreover, he is intrigued by the possibilities of rational Evolutionary Medicine.

Outside of lab Marco enjoys traveling (in very, VERY small groups). He enjoys literature, history, music and art of any age. Art also includes videogames, of course. He also loves cats; and he is reciprocated, with few exceptions.

In the future, he plans to continue doing research, possibly in an academic environment. He would love to spend some time doing his job in Japan.

Journal Club: September 26

This week, the Momeni Lab Journal Club discussed the paper "Changes in the genetic requirements for microbial interactions with increasing community complexity" by Morin, Pierce, and Dutton. Morin and colleagues studied how the genes required for E. coli growth differ when the E. coli is growing alone, in a pairwise environment, or in a full microbial community.

The authors utilized Random Barcode Transposon Sequencing (RB-TnSeq), which uses a library of mutants each of which has a single gene which has been disrupted by a transposon. If E. coli mutant strains with a disrupted gene were growing much slower than expected, that gene was determined to be important for fitness. When E. coli was growing alone, the genes whose loss caused the most negative fitness effects mostly corresponded to amino acid metabolism, resource scavenging, and energy metabolism. In contrast, when E. coli was growing in pairwise conditions, many of the genes important for growth alone were no longer needed in the presence of a partner, and several genes that were not important in the alone condition suddenly became important for growth.  Similarly, when E. coli was introduced to the full community, some genes that were important for growth alone or in the pair-wise condition were no longer important, and some previously non-important genes became important in the community.  From this, the authors drew the conclusions that E. coli’s genetic requirements for growth are altered by community complexity and that higher-order interactions may be important to the structure of communities containing E. coli

Much of the work in our lab revolves around a similar principal question: what factors can influence species coexistence in communities?  While this paper is primarily focused at the genetic level, the genes identified help give insight into the different factors necessary for growth, and how those factors change from individual to community growth. Amino acid synthesis, resource uptake, and metabolism regulation are functions that our lab takes into account when studying microbial communities and this paper provides evidence that they may critical to microbial interactions.

The link to the paper for this week can be found here:

Member Monday: Babak Momeni!

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In his research, Babak's is interested in explaining how biological complexity arises and is maintained in the context of microbial communities. By understanding the underlying interactions among microbes, can we control microbial community functions? In a search for general principles that guide how communities work, he has interest in microbial communities involved in human health, industrial applications, and the environment. He finds joy in mathematical modeling and tranquility in doing experiments, so whenever he can, he combines the two.

Outside of the lab, Babak plays soccer (mostly indoor, these days) and runs. He enjoys reading fiction (although he collects good books more than he gets to read them!). More recently, playing board games with the lab and friends has also turned into one of his favorite “activities”. 

In parallel to his research, Babak is also interested in science communication and outreach.  He has a continued interest in issues of diversity in science and fairness in science evaluation, and is a member of eLife early-career advisory group.

Member Monday: Meet Ian Boland


Ian currently works with mathematical modeling on Matlab to simulate community interactions and investigate the driving force that pushes simulated populations to coexist in communities. Outside of the lab, Ian enjoys reading, rock climbing, and spending time with friends and family. After graduation, he plans to work in quality assurance in the medical devices industry. 

Member Monday: Meet Joy Zou


As a junior Computer Science and Biochemistry double major at Boston College with a concentration in Bioinformatics, Joy is currently developing a deep-learning model that accurately predicts the level of coexistence given an initial pool of microbial species and chemical mediators. Such a model would not only eliminate the need to perform thousands of experiments or simulations but would also help the scientific community explain the frequently posed question of why species with disparate fitness can stably coexist in a community.

Outside of research, Joy enjoys running, skating, spending time with friends and family, and directing a mentorship program for undergraduate students at Boston College who are eager to primarily pursue a career in STEM. After graduating, she hopes to use the skills she has developed to complete her personal project concerning improving pharmaceutical efficiency in socio-economically disadvantaged neighborhoods such as in the Bronx. She also plans on finding a career in tech/humanitarian work to not only give back to her community in New York but to also promote overall social cohesion.

Member Monday: Meet Samantha Dyckman


Sam's current interests revolve around understanding how microbial interactions lead to community stability. Microbes are essentially everywhere, but it is not always clear how they maintain their community structure and often it can be non-intuitive what will heavily impact a community's composition and stability. Sam wants to better comprehend how positive and negative (and specifically both simultaneously) can affect the community as a whole. In order to do this Sam wants to use the model organism, E. coli,  since it is easy to genetically manipulate and also simple to culture in lab. By creating a synthetic community, she can examine how these different interactions lead to stability and better apply it to natural communities in the future. 

Outside of the lab, Sam enjoys reading when she gets the chance (aka her commute on the T each morning). When she's feeling more social, board games are another hobby of hers, and if the weather ever gets above 50 degrees, she really enjoys soccer and hiking. 

As a second year graduate student she still has many years ahead of her before earning her PhD, but once she achieves it she hopes to use her experience here to work for the Center for Disease Control (CDC). Sam wants to bridge her lab skills with more public outreach to hopefully leave a positive impact on her community. 

Member Monday: Meet Thaís de Palma

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Thaís is originally from Brazil and moved to the USA in 2016 where she works as a visiting researcher in Momeni’s lab. She has a Bachelor’s degree in Dentistry and a Master’s Degree in Oral Microbiology and Immunology from the State University of Campinas, Brazil. Thaís’ research focuses on oral microorganisms such as StreptococcusRhotiaNeisseria, and Actnomyces. Currently, employing in vitro experiments, she is investigating how these oral species interact with each other. Thaís is also taking advantage of her time in the lab to learn about Mathematical Models applied to Microbiology. She is applying to her PhD in microbiology and hopes to become a graduate student next fall. Outside the lab, Thaís enjoys traveling, cooking for her friends, and watching series.

Member Monday: Meet Lori Niehaus


As a biology and international studies major, Lori is interested in trying to understand the ways chemically-mediated microbial interactions could be used to improve human health across the globe.  Currently, she is studying the combined effect of two substances that inhibit bacterial growth - acetic acid and erythromycin.  The potential applications of this research are plentiful.  Low concentrations of acetic acid, for example, have been found to be effective in treating burns, and as resistance to penicillin increases, more and more patients are relying on erythromycin as an an antibiotic. Outside of the lab and the classroom, Lori enjoys playing intramural soccer and basketball and is currently training for the Boston Marathon!

Member Monday: Meet Kevin Chen

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Kevin is a senior currently studying the effect of inhibitors on E. coli growth rate in single and combination experiments. Outside of the lab, he is interested in cooking, spending a lot of his time watching how-to videos on Youtube and learning about different food-styles and food-cultures. After graduation, he hopes to pursue a career in computational biology; if you know of any prospective entry-level jobs in the field, feel free to contact him at!

Member Monday: Meet David Fu

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David is currently working with Marco to investigate mycotoxin degradation by Rhodococcus pyridinivorans in hope of a possible usage in bioremediation. David is also excited that they are collaborating with French scientists abroad in delineating the underlying genetic/enzymatic mechanism. He hopes to take his results and compile them into a senior thesis. Outside of lab he is applying to medical schools which he plans to begin attendance of in Fall 2018.