Picture of chemicals displayed on a shelf in a biology lab.

Fall Defenses in the Biology Department

This fall semester has been a fruitful season in the Biology Department. Three doctoral candidates –  Meining Carly Ching, Tommy Tashjian, and Antonia Vitalo, – have all successfully defended their dissertations.

Meining Carly Ching

Image courtesy of Carly Ching

During her time at Northeastern, Dr. Carly Ching worked in the lab of Dr. Veronica Godoy-Carter. Ching’s research focused on bacteria called Acinetobacter baumanniiand on its survival strategies in response to environmental stress. A. baumanniiis an opportunistic pathogen, meaning that this bacteria can cause disease in immunocompromised hosts. A. baumannii-induced illness has been particularly prevalent in areas of combat. At the same time, this pathogen has shown resistance to multiple antibiotics, raising concerns in healthcare.

Antibiotics work by causing DNA damage in bacteria, so one way to find out how A. baumannii gains drug resistance is to study how this organism repairs its DNA. In bacteria, DNA repair pathways have mostly been studied in a common laboratory species E. coli, but other bacteria often do things their own way. Ching set out to investigate how A. baumanniifixes its genetic code.

She discovered that DNA damage increased diversity within A. baumanniibacterial communities. Different cells had varying levels of a protein called RecA, which participates in DNA repair. Lower levels of RecA in some bacterial cells suggested that different A. baumanniicells reacted differently to having their DNA damaged. Some cells were repairing their DNA, but strangely, others were not.

To investigate this unexpected finding, Ching looked into how the RecA protein can affect resistance of A. baumanniito stress. She created bacterial cells that did not express any RecA, and grew them into biofilms. Biofilms are bacterial communities that populate various surfaces, often causing disease. Interestingly, Ching found that RecA-deficient biofilms were more viable that the normal biofilms.

So what are the implications of the discovery that bacterial cells express RecA differently in response to stress? This finding is of medical concern, because RecA-deficient, and thus more viable A. baumanniipopulations may be more difficult to eradicate in hospitals.

Ching’s dissertation work uncovered that stress can driveA. baumanniito phenotypic heterogeneity, forcing some cells to sacrifice their DNA repair in order to increase the fitness of the entire population.

“Other genes can be regulated in a similar way,” said Ching, who has just began her new position as a postdoctoral researcher at BU, where she studies effects of substandard antibiotics on various bacteria. Understanding how bacteria change their gene expression when treated with antibiotics will bring us closer to solving the ever-increasing menace of antibiotic resistance.

While studying stress responses in bacteria, Ching became an expert at handling her own often-stressful load of responsibilities. Working with a not-so common bacterial organism required her to test out various biochemical techniques and to be resourceful in the lab. Befitting her expertise, Ching also taught biochemistry lab throughout graduate school. She was also on the organizing committee of Boston Bacterial Meeting, volunteering her time to coordinate fundraising efforts for this student- and postdoc-run professional meetup.

A way to relieve all that stress? Working with your hands beyond the lab! During the last year of her PhD, Ching took up pottery classes. She has shared that this artsy activity can be good for scientists, as, unlike research, it almost always produces immediate and tangible results.

Congratulations to Dr. Carly Ching!


Tommy Tashjian

Image courtesy of Tommy Tashjian

Dr. Tommy Tashjian is the other recent graduate of Dr. Godoy-Carter’s lab. Her doctoral work focused on mechanisms behind antibiotic resistance, a growing problem in healthcare.

Some bacterial species are becoming increasingly impervious to antibacterial drugs, driving up mortality rates and healthcare expenses. But how do these bacteria escape the lethal effect of the drugs? The still-poorly understood mechanisms behind this issue may involve mutations in the bacterial DNA.

During her graduate career, Tashjian used the E. colibacteria to research a bacterial enzyme called DinB. This enzyme is a polymerase and participates in DNA replication. Unlike other polymerases, DinB commits many more errors when piecing together DNA. The resulting mistakes in the genetic code, or mutations, may help bacterial cells gain resistance to antibiotics.

Tashjian discovered that the activity of DinB was regulated by the protein RecA, which is also involved in DNA replication. Like all enzymes, DinB owes its functionality to its distinctive molecular shape. Tashjian used circular dichroism spectroscopy and size exclusion chromatography to confirm that RecA and DinB interacted with each other, changing the shape of DinB. This shape-shifting also altered the function of the polymerase, causing it to make fewer mistakes when assembling the DNA.

This finding led Tashjian to hypothesize that the regulation of the error-prone DinB polymerase by RecA occurs when a bacterial cell does not need to adapt to its environment, and would prefer genomic stability instead.

So what happens if antibiotics enter the picture?

Some antibacterial drugs work by causing double-stranded DNA breaks in bacterial genome. In the event of  a double-stranded DNA break, the DinB polymerase is known to help repair the genetic code. Tashjian uncovered that DinB may be involved in separating the two strands of DNA during its repair, also managing to narrow the DinB function in double-stranded DNA break repair down to just two amino acids.

Thanks to Tashjian’s work, we are now closer to understanding how bacteria regulate their DNA replication and to putting this knowledge to use towards solving the issue of antibiotic resistance.

Dr. Tashjian will now continue to study bacterial DNA replication as a post-doctoral researcher at University of Massachusetts Amherst. To the next generation of PhD students, Tashjian advises “not to tie emotions to success in science,” as any PhD journey has its highs and lows. A veteran biochemistry lab TA, Tashjian confided that managing teaching and research responsibilities can be a handful, but in the end, the department community helps form great relationships that facilitate this journey. Tashjian has herself contributed a lot to the tight-knit community of the biology department by organising summer Lab Olympics and helping new biochemistry TAs navigate teaching.

Tashjian also recommends achieving a work-life balance. For her, the “life” part has been pretty busy too. Over the first few years of her PhD program, she was involved in running “Rainbow”– a non-profit organization in Tewksbury, MA, which helps girls become better public speakers and serve the community. In addition to her efforts in promoting leadership among girls, Tashjian has also been a vital part of the Boston Bacterial Meeting fundraising committee.

Congratulations to Dr. Tommy Tashjian!


Antonia Vitalo

Dr. Antonia Vitalo conducted her dissertation research in the laboratory of Dr. Günther Zupanc, studying brown ghost fish. This fish species, native to South America, produces and detects electric signals as a mode of communication. Their spinal cord accommodates this unusual ability through cells called electromotorneurons.

In addition to communicating with electricity, brown ghost fish have an incredible ability to regenerate their brain and the spinal cord. Vitalo’s work focused on deciphering the cellular mechanisms that underlie regeneration of the spinal cord in this fish species.

Brown ghost fish react to spinal cord trauma very differently from mammals. In a mammalian spinal cord, the first response to an injury is proliferation of glial cells. These non-neural support cells of the nervous system form a glial scar at site of the injury, which emits anti-regenerative signals and, in most cases, prevents recovery.

“In a regeneration-competent species, the glial scar is more of a scaffold,” said Vitalo. This scaffold promotes regeneration.

An injured brown fish spinal cord first responds with apoptosis, or programmed cell death. The cell supply is then replenished when new cells are born and differentiate into more mature cell types. Finally, nerve cells regenerate, repairing the injury site. The electromotorneurons regenerate as well.

As brown ghost fish are a less common model of spinal cord regeneration that other animals, Vitalo first investigated whether it produces a glial scar in response to injury. She looked for chondroitin sulfate proteoglycans, which are the chief inhibitors of axons regeneration and are released by glial cells called astrocytes.

Of those inhibitory molecules, Vitalo discovered none at the spinal cord injury site. This result suggested that brown ghost fish do not form an anti-regenerative glial scar. She then tackled the question of how electromotorneurons regenerate in the fish spinal cord.

Calbindin-D28k is an important player in the nervous system. This protein of the calbindin family predictably binds calcium ions, thus regulating calcium signaling in the organism. Calbindin is critical during the developmental period in the nervous system, so Vitalo decided to see whether it may play a role in regeneration of the spinal cord.

She discovered that when compared to an intact spinal c0rd, the expression of calbindin-D28k was greater by a third, showcasing the involvement of this protein, as well as calcium signaling by extension, in spinal cord regeneration.

Vitalo’s research has helped shed light on the mysterious process of spinal cord regeneration – a feat that is beyond the mammalian grasp, but well within the norm for fishes and amphibians.

During her graduate career, Vitalo loved broadening her expertise and learning to work with a novel model organism, but she admitted that it was sometimes challenging to work with it. As brown ghost fish are only used by a handful of labs in North America, many commercially available reagents simply do not work in their tissue. To counteract those issues, Vitalo did a great deal of troubleshooting and experimenting with protocols. These skills will undoubtedly help propel her post-graduate career at pharmaceutical and biotech companies, as she returns to work in the industry.

Vitalo had already worked in the industry before she joined the Northeastern Biology PhD program. For her, this transition required a shift in mentality. As a PhD student, one often brings work home from the lab and works weekends. On top of that, Vitalo was kept extra busy when she teamed up with Dr. Erin Cram to entirely redesign the genetics lab course BIO2501, transforming it to a computer-based course.

So how did she maintain the often-elusive work-life balance that is so critical for one’s well-being? Vitalo is a runner, but not just your average neighborhood jogger. She has completed three Boston marathons, four or five marathons elsewhere, not counting many other smaller races, and undoubtedly there will be many more races to come.

Congratulations to Dr. Antonia Vitalo!