News & Events
News
A biologist’s guide to the field of quantitative bioimaging
This preprint by Senft et al. describes the different ins and outs in quantitative bioimaging. starting with sample prep up until image data acquisition, analysis, and interpretation.
Automated dispensing and fractionation of nanoparticles and viral vectors through a quantitative nanopore mesh device
Meni Wanunu & Sara Rouhanifard
Researchers introduce a nanopore device for measuring particle metrics, enhancing quality evaluation. The system, using multi-channel chips with adjustable voltage, allows precise dispensing. Automated fluid flow streamlines quality control in gene therapy production, potentially boosting success rates and reducing development times.
“Sticky” guanidinium ions enhance anion selectivity of nanopores
This “sticky-ion” approach proves versatile and can induce ion selectivity without changing the pore’s shape or surface chemistry. The potential applications include controlling molecular transport at the nanoscale, with exciting possibilities for detecting, identifying, and sequencing individual proteins using these nanopores.
Multi-channel nanopore sensing platform for single-molecule protein fingerprinting
A new multi-channel sensing platform reduces noise and increases efficiency, enhancing the ability to obtain accurate and reproducible fingerprint signatures for various proteins.
Mechanically Tunable, Compostable, Healable and Scalable Engineered Living Materials
This paper presents Mechanically Engineered Living Material with Compostability, Healability, and Scalability (MECHS) – a material that integrates these features in the form of a stretchable plastic that is simultaneously flushable, compostable, and exhibits the characteristics of paper.
Domain-swapped G20c portal protein facilitates insertion into lipid membranes for nanopore sensing
A dynamic duo of CILS Institute members! The Wanunu Lab and the Libby Lab’s newest paper “Domain-swapped G20c portal protein facilitates insertion into lipid membranes for nanopore sensing” is out in Biophysical Journal.
Machine learning for prediction of protein function and elucidation of enzyme function and control
This new paper from the Ondrechen Lab expands on the machine learning methodology of partial order optimum likelihood (POOL).
The methodology is used to predict biochemically active amino acids in the three-dimensional structures of proteins.
Every cell has the same DNA, but each cell exhibits a distinct role and function – How? Unlocking RNA’s Secrets
Learn about Professor Rouhanifard’s lab, which is dedicated to unraveling the mysteries of RNA modifications and how they are striving to understand the complexity of human cell differentiation at the RNA level. We explore the vital role of RNA in the human body, including its link to the SARS-CoV-2 vaccine. Watch now to learn about the potential therapeutic applications and the impact of curiosity-driven research.
Biochemical Activity of 17 Cancer-Associated Variants of DNA Polymerase Kappa Predicted by Electrostatic Properties
In this work, the researchers observed that POOL predictions can be used to predict which variants have decreased activity. Predictions from bioinformatic tools like SIFT, PolyPhen-2, and FATHMM are based on sequence comparisons and therefore are complementary to POOL but are less capable of predicting biochemical activity. These bioinformatic and computational tools can be used to identify SNP variants with deleterious effects and altered biochemical activity from a large data set.
Frontal plane pelvic kinematics during high velocity running: Association with hamstring injury history
Injured sprinters displayed significantly greater mediolateral motion and asymmetry during stances than healthy counterparts.
Determining the effects of AR/VR HMD design parameters (mass and inertia) on cervical spine joint torques
Based on these results, to minimize joint torques, headsets should be designed so that both display mass and anterior display mass distance are minimized.
A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein
This study combines single molecule nanopore experiments and all-atom MD simulations to examine the electric-field-driven unfolding during the translocation through a model pore of individual protein knots important for methylating tRNA.
E-cigarette Aerosol Exposure Effect on Bone Biomechanical Properties in Murine Models
The findings suggest that, although vaping can result in a higher bone volume, this bone is weaker than average.
Professor Shansky's Recent Book Chapters
Ratiometric fluorescence sensing and quantification of circulating blood sodium sensors in mice in vivo
In this work, the researchers introduce ratiometric diffuse in vivo flow cytometry (R-DiFC) for quantitative measurement of circulating fluorescent red blood cell (fRBC) sensors for systemic blood sodium levels.
Kinetics and mechanism of halide exchange in reactions of CpRu(PPh3)2Cl with alkyl halides: evidence for radical pairs
Findings from CILS member Sijia Dong and colleagues: Density functional theory calculations on potential intermediates suggests that a pathway leading to CpRu(PPh3)(Cl)(Br)˙ is more likely than oxidative addition, which is preferred in reactions of 1 with bromoethane.
Practical solutions for including Sex As a Biological Variable (SABV) in preclinical neuropsychopharmacological research
This new paper emphasizes the importance of considering sex as a biological variable in preclinical research, providing practical guidance and debunking common concerns. It discusses the impact on experimental design, hormonal fluctuations, behavioral experiments, and therapeutic drug development.
New treatment for ovarian cancer will use lasers to target chemo-resistant cells
Professor Spring, whose lab focuses on biomedical physics, has received a $2.7 million grant to develop a new treatment for ovarian cancer that will use lasers to spot and target chemo-resistant cancer cells and boost a patient’s immune system.
Northeastern’s Tao Sun overcomes barriers to brain drug delivery with focused ultrasound
One of our newest CILS members, Tao Sun, is conducting fantastic research on delivering drugs through the blood-brain barrier! Read about how ultrasound research can open opportunities for improving the immune system in this article by Research at NU.
International Institute for Nanotechnology announces distinguished Kabiller Prize winners
Ke Zhang is the recipient of the Kabiller Rising Star Award. This $2,000 award, established in 2021, celebrates outstanding contributions by early career faculty.
His research offers fundamental insights into the interactions of new nanomaterials with living systems, and he has used this knowledge to develop practical applications that benefit humanity. His work has promising implications on the development of novel gene regulation therapeutics in diseases like non-small cell lung carcinoma and Duchenne muscular dystrophy.
Functional annotation of haloacid dehalogenase superfamily structural genomics proteins
This study examines HAD superfamily proteins, predicting and confirming functions through chemical properties analysis. Substrate promiscuity is observed in sugar phosphatases.
Cortical microvascular blood flow velocity mapping by combining dynamic light scattering optical coherence tomography and two-photon microscopy
Professor Abbas Yaseen and team developed a framework to co-register microvascular blood flow data from DLS-OCT with 2PM angiograms, enabling precise analysis of cerebral blood flow distribution in mice.
Sensor Synthesis and Storage Protocol
This protocol explains the fabrication of DNA nanosensors with pHAb dye used for stability analysis, its characterization, and the detailed protocol of the DNA scaffold stability study over a period. Here, the DNA nanosensor and Acetylcholinesterase (AchE) enzyme were analyzed separately for the stability study. Collaegue: CILS Founder Heather Clark
Researcher uses gene regulation to improve drug delivery and treatment of rare genetic diseases
Professor Ke Zhang is researching a new drug delivery method using oligonucleotides to treat Duchenne Muscular Dystrophy (DMD), with potential applications in other genetic diseases, offering hope for more efficient treatments.
Exploring a library of water-soluble polymers as abiotic phytoremediation agents for treating (Pseudo)metal ion-contaminated soil
Ke Zhang
Findings from CILS member Ke Zhang and colleagues: Of 11 water-soluble polymers, polyethyleneimine is the most potent inhibitor of metal absorption. Polymers with such effects may be used to reduce the contamination of (pseudo)metals in crops.
Ionically Active MXene Nanopore Actuators
Wanunu Lab
From Wanunu Lab, Mehrnaz Mojtabavi’s latest work that shows how nanopores in MXene layers, when subjected to a transverse electric field, can change their thickness in a reversible manner.
Bajpayee Awarded NSF CAREER Grant for Drug Delivery Biomaterials
Ambika Bajpayee
BioE Assistant Professor Ambika Bajpayee received a $630K NSF CAREER Award for “Developing electrically charged biomaterials for targeted drug delivery to negatively charged complex tissue environments.” Her research will investigate how to improve drug delivery in tissues within the human body that are not receptive to systemic or local drug delivery methods due to their high negative charge density and lack of blood vessels by using charge interactions.
Niedre and Bellini Receive $2.7M Grant from the National Cancer Institute
Mark Niedre
CILS member and bioengineering professor Mark Niedre was awarded a $2.7M grant for 5 years along with co-PI Chiara Bellini. The grant project is titled "Continuous, Non-Invasive Optical Monitoring of Circulating Tumor Cell-Mediated Metastasis in Awake Mice".
This Ink Is Alive and Made Entirely of Microobes
Neel Joshi
From The New York Times: Scientists have created a bacterial ink that reproduces itself and can be 3D-printed into living architecture.
Simple Affinity-Based Method for Concentrating Viruses from Wastewater Using Engineered Curli Fibers
Neel Joshi
New paper from the Joshi Lab and Pinto Lab focuses on a new, simple procedure for concentrating viruses from wastewater using bacterial biofilm protein nanofibers known as curli fibers.
Steven Lopez and Tovah Day Win Pretigious NSF CAREER Grants
Tovah Day and Steven Lopez
Two CILS members have been awarded the early-career grant that is based off of the high potential of current and expected research.
Rapid Identification of DNA Fragments through Direct Sequencing with Electro-Optical Zero-Mode Waveguides
Meni Wanunu
Latest from the Wanunu Lab: A new device for electrical capture of DNA into Zero-Mode Waveguides (ZMWs), which enables low-input DNA capture for future studies.
Regeneration: A matter of nerves
James Monaghan
Unravelling roles of error-prone DNA polymerases in shaping cancer genomes
Tovah Day
New review article from Tovah Day and collaborators discusses how mutational cancer cells may be molded from DNA repair defects by error-prone polymerases.
ZYX-1/Zyxin plays a minor role in oocyte transit through the spermatheca in C. elegans
Erin Cram
New paper from the Cram Lab suggests ZYX-1/Zyxin may regulate spermathecal contraction magnitude or timing of spermathecal bag contraction and/or spermathecal-uterine valve dilation.
Detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct, long-read sequencing
Sara Rouhanifard & Meni Wanunu
New paper from the Rouhanifard Lab and Wanunu Lab shows how they developed a semi-quantitative method for mapping pseudouridylated sites with high confidence directly on mammalian mRNA transcripts.
Frogs can regrow amputated limbs after being treated with mix of drugs, new research finds
James Monaghan
Read associate director James Monaghan’s commentary to CNN about new regeneration research that “is exciting because it shows that endogenous regenerative processes can be enhanced by a short application of a drug cocktail.”
"From Sensing to Chemical Imaging" Editorial from Director Clark
Heather Clark
“By adding the chemical content to the image, we have the potential to provide information on the amplitude, location, and timing of analyte levels─combining the strengths of sample analysis and imaging into one powerful technique that could change our protocols for disease diagnosis and study…”
MOCA: a systematic toolbox for designing and assessing modular functional near-infrared brain imaging probes
Qianqian Fang
New paper from the Fang Lab on a new modular probe design platform – designed to help users manevuer the obstacles of module- and probe-parameter selection and fine-tuning.
Measuring Biochemicals in the Body at the Nanoscale: A Conversation with Heather Clark
Heather Clark
In this episode of the “Stories from the NNI” podcast, Heather Clark, Professor of Bioengineering and Chemistry at Northeastern University, discusses her work on developing biosensors to measure, at the nanoscale, how biochemicals are regulated in the body.
Steven Lopez one of four Co-Investigators for the newly launched Institute for Data-Driven Dynamical Design.
Steven Lopez
The new institute, funded $15.5 million by the NSF, aims to address the challenge of predicting dynamical processes in materials with a focus on discovering fundamentally new mechanisms and pathways.
Solving Quantum Riddles: Dr. Sijia Dong is Using Machine-Learning to Overcome Challenges in Quantum Chemical Computation
Sijia Dong
In a recent publication in Chemical Science, Dr. Dong and co-authors developed a new computational strategy that can be used to understand how complex materials behave when they are exposed to sun light.
New Nanosensor Holds Promise for Diagnosing, Treating Neurological Disease
Heather Clark, James Monaghan
CILS founders developed a DNA-based nanosensor that detects a specific neurotransmitter, acetylcholine, as it’s released and picked up by target cells in living animals.
Bryan Spring Named A Scialog: Advancing Bioimaging Fellow
Bryan Spring
For early-career researchers chosen to address challenges involved in enhancing high-resolution imaging of tissue.
Special Issue Tissue Engineering Features Bajpayee Lab Research
Tissue Engineering June 2021 special issue cover features the Bajpayee Lab’s injectable shape-memory cryogels for cartilage defect repair.
Heather Clark Named As AIMBE Fellow
Dr. Clark was nominated for her development of nanoscale optical probes for chemical imaging within live cellular and tissue environments. This honor is immense for medical and biological engineers across the country, as only the top two percent are recognized with a fellowship.
Ambika Bajpayee Nominated as Biomaterials Science Emerging Investigator
Bajpayee’s paper “Milk exosomes with enhanced mucus penetrability for oral delivery of siRNA” earned her a nomination for Biomaterials Science Emerging Investigator on the 2021 list.
Cellaria Inc. Partners with the Spring Lab to Advance New Photomedicine Therapies for Key Cancers with NIH R01 Grant
Bryan Spring
The grant provides $3.2M funding to develop precision therapeutics closely tailored to the requirements of specific patient populations. The Spring Lab uses Cellaria’s next generation, patient-derived, customized cell models that boost the effectiveness of in vitro studies.
Bajpayee Lab receives National Institute of Arthritis and Musculoskeletal and Skin Diseases R01 Award
The Bajpayee Lab was awarded the NIAMS R01 for their work on charge based drug delivery to cartilage.
Professor Spring Uses Light to Accelerate Treatment of Drug-resistant Cancers
Assistant professor Bryan Spring develops photodynamic light-based therapies that both target the malignant cells and stop the signaling between them that sparks new tumor growth.
Events
Enhance Your Imaging Capability with CILS
November 18th, 2022 2-3pm
Virtual
CILS Seminar & Demo: Nanosurf DriveAFM
Join us for an information session on the features of the Nanosurf Drive AFM. During the seminar, participants will hear about applications for projects and how AFM pairs with confocal microscopy, followed by a student presentation.
June 29th, 2022
Seminar: 12-1:30pm
Demo: 1:30-2:30pm
Virtual
Tissue Clearing Webinar
Come join us on February 10th, 2023 at 1-2 pm (EST)📅 to learn more about how to improve your microscopy images of thick samples via Tissue Clearing 🔬
Our imaging scientist Eun will explain why tissue clearing is important to boost microscopy signal from your thick samples, and will discuss different methods and applications.
Register here: ➡ https://lnkd.in/ey5eg9y2 ⬅
CILS Seminar: Photoacoustics from VisualSonics
Join us for an information session on the features of the VisualSonics Vevo LAZR-X. During the seminar, participants will hear about applications for projects in the fields of oncology, molecular biology, cardiology, neurobiology, etc, followed by a student presentation.
February 24th, 2022 12-1:30pm
Virtual
CILS Seminar: arivis™️ Imaging Software
Join this seminar to learn how to make image analysis from microscopes more straightforward. An arivis representative will be presenting on topics such as image segmentation, multiview registration, storyboard, colocalization, and image processing (denoise, decon, etc).
December 14th, 2021 12-1pm
Virtual
CILS Seminar: Flow Cytometry
Join us for an information session on the features of our Beckman cell sorter and analyzer. During the seminar, participants will hear from users about their experiences and applications for a variety of projects, followed by a student presentation.
September 28th, 2021 12-1:30pm
Virtual
CILS Seminar: Bruker BioSpec™ 3T MRI
The seminar will cover how preclinical MR offers longitudinal observation/measurement of disease processes, an overview of components and process for preclinical MR, and review of methods and data obtained in preclinical MR.
Following the talk, Kristine Ma, PhD candidate from the Clark Lab, will present on DNA-based pH-responsive MR contrast agents.
June 9th, 2021 12-1:30pm
Virtual
CILS Seminar: Zeiss Lightsheet Z1
Join us for an informational session to learn about the features of the Zeiss Lightsheet Z1 hosted by Zeiss. During the week following the event, participants will have FREE access to microscope demonstrations in our core facility.
April 8th, 2021 12-1:30pm
Virtual
Film Screening: Picture A Scientist
The Institute for Chemical Imaging of Living Systems (CILS) hosted a screening of Picture A Scientist (https://www.pictureascientist.com/) to kick off our monthly educational series. This film is a documentary raising visibility around gender bias and racism in science and was available to the Northeastern community for online viewing January 28-30, 2021.
January 28-30, 2021
Virtual
Our facility
Interdisciplinary Science and Engineering Complex
ISEC 080, 805 Columbus Ave, Boston, MA, 02115