Making Great Strides in Research

MAKING GREAT STRIDES RESEARCH

A remora fish readies to feed and skim along a whale body. Photo credit: Stanford University, Cascadia Research Collective and Journal of Experimental Biology

International Study Uncovers Secret Surfing Life of Remoras

Sticking to the bodies of sharks and other larger marine life is a well-known specialty of remora fishes (Echeneidae), accomplished through super-powered suction disks on their heads. But now, NJIT researchers have led a study that has fully documented the “suckerfish” in hitchhiking action below the ocean’s surface, uncovering a more refined skill set the fish uses for navigating intense hydrodynamics aboard a 100-foot blue whale (Balaenoptera musculus).

In the Journal of Experimental Biology, an international research team, studying the complex fluid environments of blue whales off the California coast, describes successfully capturing the first-ever continuous recording of remora behavior on their host, using advanced biosensing tags with video-recording capabilities. Brooke Flammang, assistant professor of biology at NJIT and the study’s corresponding author, calls the recording “incredible,” as little has been known previously “about how remoras behave on their hosts in the wild over any prolonged period of time.”

The study shows remoras successfully hitchhike aboard baleen whales more than 30 times their size by selecting the most flow-optimal regions on the whale’s body to stick to, such as behind the whale’s blowhole and dorsal fin, where drag resistance for the fish is reduced by as much as 84%. The researchers also discovered remoras can freely move around to feed and socialize even as their whale host hits burst speeds of more than 5 meters per second, by utilizing surfing and skimming behaviors along special low-drag traveling lanes that exist just off the surface of the whale’s body. The team is using their new insights into the remora’s preferred low-drag attachment locations to better inform how they might tag and track whales in studies to come. n

NJIT is designated an R1 research institution, for “Very High Research Activity,” by the Carnegie Classification®.

Removing a Roadblock in the Genetic Therapy Revolution

Cell and gene therapies represent a new frontier in the already complex world of biotechnology. However, the distribution and adoption of these promising therapies are hindered by significant manufacturing challenges. NJIT’s New Jersey Innovation Institute (NJII) has launched a new ultramodern facility to help the industry overcome these challenges. The facility does business as “BioCentriq.” The scientists and engineers at BioCentriq work directly with biopharmaceutical companies to perfect their manufacturing processes, develop their processes for scale-up and produce supplies for their preclinical testing and clinical trials.

BioCentriq was formed incollaboration with technology providers, biopharmaceutical companies, regulatory agencies and economic development organizations. Its business model allows for the client’s own scientists and engineers to work alongside BioCentriq experts to foster stronger collaboration and faster technology transfer.

Cellular and genetic therapies work by delivering cells or genetic material that have been engineered to elicit a therapeutic effect in a patient, such as reprogramming the body’s immune system to detect and fight certain types of cancers, neurological disorders and other autoimmune diseases. This approach may also be used to fight infectious viruses.

The challenges in developing and manufacturing these drugs consistently and at the necessary scale have slowed their entry to the market and made them cost-prohibitive. BioCentriq aims to speed up the production of these medicines while maintaining clinical safety standards and reducing costs.

Cell and gene therapy work requires a highly trained workforce. To address current shortages in manufacturing talent, NJIT offers a 30-credit professional master’s program in cell and gene therapy, and BioCentriq provides customized training for biotechnology companies. n

Left: BioCentriq Senior Vice President and General Manager Haro Hartounian at the company’s South Brunswick, N.J., facility, where NJII scientists work with drug developers to streamline the processing of new cell and gene therapies.

Machine-Learning Method Finds Therapeutic Targets in Pediatric Genome

NSF CAREER Award for Simplifying Crowdsourced Requests

Ateam of researchers from NJIT and Children’s Hospital of Philadelphia (CHOP) have developed an algorithm through machine learning that helps predict sites of DNA methylation — a process that can change the activity of DNA without changing its overall structure — and could identify disease-causing mechanisms that would otherwise be missed by conventional screening methods. Their paper was published online by Nature Machine Intelligence.

DNA methylation is involved in many key cellular processes and is an important component in gene expression. Errors in methylation can be linked to a variety of human diseases, and while genomic sequencing tools are effective at pinpointing polymorphisms that may cause a disease, those same methods are unable to capture the effects of methylation because the individual genes still look the same.

To address this issue, the researchers turned to deep learning. Zhi Wei, professor of computer science at NJIT, worked with fellow senior co-author of the study, Hakon Hakonarson, M.D., director of the Center for Applied Genomics at CHOP, and his team to develop a deep-learning algorithm that could predict where these sites of methylation happen, which would then help researchers determine the effect they might have on certain nearby genes.

Wei calls his software Deep6mA and led the development of a neural network, a machine-learning model that attempts to learn in similar ways to a brain. Neural networks have been utilized in cellular research before, but this is their first application to study DNA methylation sites on natural multicellular organisms.

Deep6mA was able to identify 6mA methylation sites down to the resolution of a single nucleotide, or basic unit of DNA. Even in this initial confirmation study, the researchers were able to visualize regulatory patterns that they had been unable to observe using previously existing methods. n

Senjuti Basu Roy, assistant professor of computer science and an expert on optimizing machine-learning techniques, received a prestigious National Science Foundation CAREER award for her research addressing inefficiencies of deploying tasks in crowdsourced labor services. The award acknowledges early-career activities of scholars who integrate research and education in the context of their organizations. Crowdsourcing is the concept of solving complicated jobs by dividing the work among large groups of dispersed workers, who are often lay people rather than professionals. Unfortunately, the process of planning and deploying tasks through crowdsourcing can be almost as complicated as the job itself, in that there is little to no help for requesters in Senjuti Basu Roy deciding how to organize the workforce, in what style and in what structure to satisfy deployment parameters, Basu Roy explained.

Basu Roy is developing middleware called SLOAN (short for Scalable, decLarative, Optimization-driven, Adaptive and uNified) to make life easier for the task deployers. SLOAN will have components for analyzing workers’ preferences and availability, modeling and recommending deployment strategies for batches of requests, and aggregating results to estimate the quality of the completed tasks undertaken by the workers. n

Ushering in a Carbon-Neutral Economy

Siva Nadimpalli The stakes for next-generation batteries that are high-capacity, long-lived and affordable could not be higher, as the promise of a carbon-neutral economy depends on their success. While newer batteries can store 10 times as much energy as their graphite predecessors, they fade too quickly. The breakdown occurs at the interfaces between the polymers and the active materials that sustain electrochemical reactions; when these particles become electrically isolated, a battery’s charging capacity and overall longevity are curtailed.

Siva Nadimpalli, director of NJIT’s Micro and Nano Mechanics Laboratory, uses novel techniques to reveal how battery electrodes break down in real time, rather than after they degrade. His custom-made cell enables electrochemical and stress measurements simultaneously, and his thin-film electrodes — 10,000 times thinner than a human hair — capture real-time, uniform readings when a cell is running.

He aims to advance to development of multiphysics mathematical models, which capture a battery’s mechanical behavior and the electrochemical activity of its electrodes, to predict how mechanical forces impact chemical reactions in battery materials, and to assess their corresponding electrical performance on, say, the current supplied by batteries at any voltage. n