Emre Firlar

ORCID: 0000-0003-0190-6528
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About
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Research Areas
  • Bacterial Genetics and Biotechnology
  • RNA and protein synthesis mechanisms
  • Geomagnetism and Paleomagnetism Studies
  • Bacteriophages and microbial interactions
  • Nanoparticle-Based Drug Delivery
  • Magnetic and Electromagnetic Effects
  • Advanced Electron Microscopy Techniques and Applications
  • Iron Metabolism and Disorders
  • Iron oxide chemistry and applications
  • Trace Elements in Health
  • RNA modifications and cancer
  • Graphene and Nanomaterials Applications
  • Electron and X-Ray Spectroscopy Techniques
  • Calcium Carbonate Crystallization and Inhibition
  • Nanopore and Nanochannel Transport Studies
  • Antibiotic Resistance in Bacteria
  • Virus-based gene therapy research
  • Bacterial biofilms and quorum sensing
  • Lipid Membrane Structure and Behavior
  • Nanoparticles: synthesis and applications
  • Kidney Stones and Urolithiasis Treatments
  • Pancreatic function and diabetes
  • Clay minerals and soil interactions
  • RNA Interference and Gene Delivery
  • Geophysical and Geoelectrical Methods

Rutgers, The State University of New Jersey
2019-2025

Quantitative BioSciences
2019-2024

Bristol-Myers Squibb (United States)
2024

Rütgers (Germany)
2019-2022

Rutgers Sexual and Reproductive Health and Rights
2019-2022

University of Illinois Chicago
2016-2021

Ames National Laboratory
2014-2016

Stevens Institute of Technology
2010-2015

In bacteria, transcription and translation are coupled processes in which the movement of RNA polymerase (RNAP)-synthesizing messenger (mRNA) is coordinated with first ribosome-translating mRNA. Coupling modulated by factors NusG (which thought to bridge RNAP ribosome) NusA. Here, we report cryo-electron microscopy structures Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between ribosome active-center P site. Structures TTCs short show a...

10.1126/science.abb5317 article EN Science 2020-08-20

Abstract Nanocarrier administration has primarily been restricted to intermittent bolus injections with limited available options for sustained delivery in vivo. Here, we demonstrate that cylinder-to-sphere transitions of self-assembled filomicelle (FM) scaffolds can be employed monodisperse micellar nanocarriers improved bioresorptive capacity and modularity customization. Modular assembly FMs from diverse block copolymer (BCP) chemistries allows situ gelation into hydrogel following...

10.1038/s41467-018-03001-9 article EN cc-by Nature Communications 2018-02-06

Magnetotactic bacteria biomineralize ordered chains of uniform, membrane-bound magnetite or greigite nanocrystals that exhibit nearly perfect crystal structures and species-specific morphologies. Transmission electron microscopy (TEM) is a critical technique for providing information regarding the organization cellular in these microorganisms. However, conventional TEM can only be used to image air-dried vitrified removed from their natural environment. Here we present correlative scanning...

10.1038/srep06854 article EN cc-by-nc-nd Scientific Reports 2014-10-31

Recently, two-dimensional (2D) nanomaterials are gaining tremendous attention as novel antibacterial platforms to combat against continuously evolving antimicrobial resistance levels. Among the family of 2D nanomaterials, black phosphorus (BP) nanosheets have demonstrated promising potential for biomedical applications. However, there is a need gain nanoscale insights activity BP which lies at center technical challenges.

10.2147/ijn.s237816 article EN cc-by-nc International Journal of Nanomedicine 2020-04-30

Magnetosome biomineralization in magnetotactic bacteria was observed by keeping the alive using graphene liquid cell transmission electron microscopy.

10.1039/c8nr08647h article EN Nanoscale 2018-12-19

Abstract Calcium oxalate (CaOx) is the major phase in kidney stones and primary calcium storage medium plants. CaOx can form crystals with different lattice types, water contents, crystal structures. However, conditions mechanisms leading to nucleation of particular are unclear. Here, liquid‐cell transmission electron microscopy atomistic molecular dynamics simulations used study situ at conditions. The observations reveal that rhombohedral monohydrate (COM) nucleate via a classical pathway,...

10.1002/adfm.202007736 article EN Advanced Functional Materials 2021-02-26

The double membrane architecture of Gram-negative bacteria forms a barrier that is impermeable to most extracellular threats. Bacteriocin proteins evolved exploit the accessible, surface-exposed embedded in outer deliver cytotoxic cargo. Colicin E1 bacteriocin produced by, and lethal to, Escherichia coli hijacks (OMPs) TolC BtuB enter cell. Here, we capture colicin translocation domain inside its receptor, TolC, by high-resolution cryo-electron microscopy obtain first reported structure...

10.7554/elife.73297 article EN cc-by eLife 2022-02-24

In Gram-negative bacteria, the enzymatic modification of Lipid A with aminoarabinose (L-Ara4N) leads to resistance against polymyxin antibiotics and cationic antimicrobial peptides. ArnC, an integral membrane glycosyltransferase, attaches a formylated form lipid undecaprenyl phosphate, enabling its association bacterial inner membrane. Here, we present cryo-electron microscopy structures ArnC from S. enterica in apo nucleotide-bound conformations. These reveal conformational transition that...

10.1101/2025.01.29.634835 preprint EN cc-by-nc-nd bioRxiv (Cold Spring Harbor Laboratory) 2025-01-30

In the modern construction industry, large gypsum (CaSO4·2H2O) boards are manufactured through a two-step procedure, which features heating of fine powders to form intermediate plaster Paris (bassanite, CaSO4·0.5H2O) followed by hydration phase final formed product. Here, we explore novel pathway toward fabrication microneedles that bypasses formation bassanite phase. Using in situ liquid transmission electron microscopy, dynamic behavior calcium sulfate solution is investigated at nanoscale...

10.1021/acsanm.8b00739 article EN ACS Applied Nano Materials 2018-09-27

Abstract Rheological behavior of aqueous suspensions containing nanometer-sized powders is relevance to many branches industry. Unusually high viscosities observed for nanoparticles compared those micron size cannot be explained by current viscosity models. Formation so-called hydration layer on alumina in water was hypothesized, but never experimentally. We report here the direct visualization with fluid cell situ. observe formed over particle aggregates and show that such hydrated...

10.1038/srep09830 article EN cc-by Scientific Reports 2015-05-21

Occlusive thrombosis is a central pathological event in heart attack, stroke, thromboembolism, etc. Therefore, pharmacological thrombolysis or anticoagulation used for treating these diseases. However, systemic administration of such drugs causes hemorrhagic side-effects. there significant clinical interest strategies enhanced drug delivery to clots while minimizing effects. One strategy by using drug-carrying nanoparticles surface-decorated with clot-binding ligands. Efforts this area have...

10.1039/d0nr03633a article EN Nanoscale 2020-01-01

ABSTRACT Poly(ethylene glycol) (PEG) can serve as an electron‐beam (e‐beam) resist to modulate protein adsorption on and cell adhesion surfaces. PEG preferentially crosslinks under e‐beam irradiation create microgels with controllable properties. Here, atomic‐force, scanning electron, confocal microscopies are used study discrete formed from solvent‐cast thin films by focused e‐beams energies between 2 30 keV point doses 10 1000 fC. Consistent experimental findings, Monte Carlo simulation of...

10.1002/polb.23367 article EN Journal of Polymer Science Part B Polymer Physics 2013-08-26

Background: Nanoscale surface roughness has been suggested to have antibacterial and antifouling properties. Several existing models attempted explain the mechanism of nanoscale rough surfaces without direct observation. Here, conventional liquid-cell TEM are implemented observe bacteria/surface interaction. The visualization such interactions enables inference possible mechanisms. Methods Results: Nanotextures synthesized on biocompatible polymer microparticles (MPs) via plasma etching....

10.2147/ijn.s232230 article EN cc-by-nc International Journal of Nanomedicine 2020-03-01

We use focused electron beams to create surface-patterned biotinylated poly(ethylene glycol) microgels which molecular beacon probes are immobilized viabiotin–streptavidin binding. hypothesize that immobilizing highly hydrated will maintain the high performance typical of untethered free in solution. Monte Carlo simulations show microgel mesh size resulting from radiation crosslinking is non-uniform and approaches infinity at microgel–water interface. This structure important because...

10.1039/c1sm06702h article EN Soft Matter 2012-01-01

The ribonuclease FttA mediates factor-dependent transcription termination in archaea

10.1101/2023.08.09.552649 preprint EN bioRxiv (Cold Spring Harbor Laboratory) 2023-08-10

Islet cell transplantation is one of the key treatments for type 1 diabetes. Understanding mechanisms insulin fusion and exocytosis are utmost importance improvement current islet treatment These phenomena have not been fully evaluated due either to lack proper dynamic imaging, or preservation during imaging at nanoscales.By maintaining native environment pancreatic β-cells between two graphene monolayer sheets, we were able monitor subcellular events using in situ liquid (GLC)-transmission...

10.2147/ijn.s169506 article EN cc-by-nc International Journal of Nanomedicine 2019-01-01

Adeno-associated viruses (AAVs) are used as in vivo gene-delivery vectors gene-therapy products and have been heavily investigated for numerous indications. Over 100 naturally occurring AAV serotypes variants isolated from primate samples. Many reports described unique properties of these (for instance, differences potency, target cell or evasion the immune response), despite high amino-acid sequence conservation. AAVhu.37 is interest clinical applications owing to its proficient...

10.1107/s2053230x20000308 article EN Acta Crystallographica Section F Structural Biology Communications 2020-02-01

Abstract In a rapidly warming world, we ask, “What limits the potential of marine diatoms to acclimate elevated temperatures?,” group ecologically successful unicellular eukaryotic photoautotrophs that evolved in cooler ocean and are critical food webs. To this end, examined thermal tolerance mechanisms related photosynthesis sequenced transformable model diatom Phaeodactylum tricornutum . Data from transmission electron microscopy (TEM) fatty acid methyl ester‐gas chromatography mass...

10.1111/gcb.15612 article EN Global Change Biology 2021-03-22

Abstract Rho and NusG mediate factor-dependent transcription termination in Escherichia coli . Here, we report preparation of complexes functional from RNA polymerase (RNAP), Rho, NusG, synthetic nucleic-acid scaffolds, cryo-EM structures complexes. The show that pre-termination contain a closed-ring hexamer, have threaded through the central channel 60 nt interacting sequence-specifically with exterior 6 oriented relative to RNAP such ATP-hydrolysis-dependent translocation by exerts...

10.1101/2022.08.29.505764 preprint EN bioRxiv (Cold Spring Harbor Laboratory) 2022-08-29
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