assessing-lost-fraction-diversity-abundance-mass-microplastics-1-300

Assessing the Lost Fraction: Diversity, Abundance, and Mass of Microplastics (1-300 &#181;m) in Aquatic Systems

The protocol presented here enables the quantification of microplastics (MPs) as small as ~1&#8239;&#181;m in diameter, accurate identification of polymer ...

Stony Brook University

The addition of hydroxyl radicals to the C8 position of guanine can lead to the formation of a 2,6-diamino-4-hydroxy-5-formamido-2'-deoxypyrimidine (Fapy-dG) lesion, whose endogenous levels in cellular DNA rival those of 8-oxo-7,8-dihydroxy-2'-deoxyguanosine. Despite its prevalence, the structure of duplex DNA containing Fapy-dG is unknown. We have prepared an undecameric duplex containing a centrally located β-cFapy-dG residue paired to dC and determined its solution structure by high-resolution NMR spectroscopy and restrained molecular dynamic simulations. The damaged duplex adopts a right-handed helical structure with all residues in an anti conformation, forming Watson-Crick base pair alignments, and 2-deoxyribose conformations in the C2'-endo/C1'-exo range. The formamido group of Fapy rotates out of the pyrimidine plane and is present in the Z and E configurations that equilibrate with an approximate 2:1 population ratio. The two isomeric duplexes show similar lesion-induced deviations from a canonical B-from DNA conformation that are minor and limited to the central three-base-pair segment of the duplex, affecting the stacking interactions with the 5-lesion-neighboring residue. We discuss the implications of our observations for translesion synthesis during DNA replication and the recognition of Fapy-dG by DNA glycosylases.

Solution structure of duplex DNA containing a β-carba-Fapy-dG lesion.

Cellular respiration and ionizing radiation generate 5',8-cyclo-2'-deoxyribonucleosides, a special type of DNA damage that involves two modifications in the same nucleotide. These lesions evade the action of base excision glycosylases, and their removal is a function of the nucleotide excision repair pathway. Diastereomeric 5',8-cyclo-2'-deoxyadenosine blocks mammalian DNA replication, diminishes the levels of DNA transcription, and induces transcriptional mutagenesis. Using solution state NMR spectroscopy and restrained molecular dynamics simulations, we have determined the structure of an undecameric DNA duplex having a centrally located (5'S)-5',8-cyclo-2'-deoxyadenosine residue paired to T. The damaged duplex structure is a right-handed helix having Watson-Crick base-pair alignments throughout, and 2-deoxyribose puckers within the B-form conformation. Only small structural perturbations are observed at the lesion-containing and 5'-flanking base pair. The 2-deoxyribose of the damaged nucleotide adopts the O4'-exo conformation, and the S-cdA·T base pair is propeller twisted. The 5'-lesion-flanking base is tilted forming a significantly buckled base pair with its partner guanine. Analysis of UV-melting curves indicates mild thermal and thermodynamic destabilization on the damaged duplex. The S-cdA·T duplex structure shows many similarities to and some intriguing differences from the recently reported structure of an S-cdG·dC duplex³¹ that suggest different lesion site dynamics.

Structure and stability of duplex DNA containing (5'S)-5',8-cyclo-2'-deoxyadenosine: an oxidatively generated lesion repaired by NER.

A new method to measure growth rates of individual photoautotrophic cells by combining stable isotope probing (SIP) and single-cell resonance Raman microspectrometry is introduced. This report explores optimal experimental design and the theoretical underpinnings for quantitative responses of Raman spectra to cellular isotopic composition. Resonance Raman spectra of isogenic cultures of the cyanobacterium,  sp., grown in C-bicarbonate revealed linear covariance between wavenumber (cm) shifts in dominant carotenoid Raman peaks and a broad range of cellular C fractional isotopic abundance. Single-cell growth rates were calculated from spectra-derived isotopic content and empirical relationships. Growth rates among any 25 cells in a sample varied considerably; mean coefficient of variation, CV, was 29 ± 3% (σ/[Formula: see text]), of which only ~2% was propagated analytical error. Instantaneous population growth rates measured independently by  fluorescence also varied daily (CV ≈ 53%) and were statistically indistinguishable from single-cell growth rates at all but the lowest levels of cell labeling. SCRR censuses of mixtures prepared from  sp. and  (a diatom) populations with varying C-content and growth rates closely approximated predicted spectral responses and fractional labeling of cells added to the sample. This approach enables direct microspectrometric interrogation of isotopically- and phylogenetically-labeled cells and detects as little as 3% changes in cellular fractional labeling. This is the first description of a non-destructive technique to measure single-cell photoautotrophic growth rates based on Raman spectroscopy and well-constrained assumptions, while requiring few ancillary measurements.

Single-Cell Growth Rates in Photoautotrophic Populations Measured by Stable Isotope Probing and Resonance Raman Microspectrometry.

The near exponential proliferation of published Raman microspectroscopic applications over the last decade bears witness to the strengths and versatility of this technology. However, laser-induced fluorescence often severely impedes its application to biological samples. Here we report a new approach for near complete elimination of laser-induced background fluorescence in highly pigmented biological specimens (e.g., microalgae) enabling interrogation by Raman microspectroscopy. Our simple chemiphotobleaching method combines mild hydrogen peroxide oxidation with broad spectrum visible light irradiation of the entire specimen. This treatment permits observing intracellular distributions of macromolecular pools, isotopic tracers, and even viral propagation within cells previously not amenable to Raman microspectroscopic examination. Our approach demonstrates the potential for confocal Raman microspectroscopy becoming an indispensable tool to obtain spatially-resolved data on the chemical composition of highly fluorescent biological samples from individual cells to environmental samples.

Tear Down the Fluorescent Curtain: A New Fluorescence Suppression Method for Raman Microspectroscopic Analyses.

 is a cosmopolitan member of the marine phytoplankton. This species' capacities for carbon sequestration and sulfur mobilization make it a key player in oceanic biogeochemical cycles that influence climate on a planetary scale. Seasonal  blooms are abruptly terminated by viral epidemics caused by a clade of large DNA viruses collectively known as coccolithoviruses (EhVs). EhVs thereby mediate a significant part of material and energy fluxes associated with  population dynamics. In this study, we use spontaneous Raman microspectroscopy to perform label-free and non-invasive measurements of the macromolecular composition of individual virions and  host cells. Our novel autofluorescence suppression protocol enabled spectroscopic visualization of evolving macromolecular redistributions in individual  cells at different stages of EhV infection. Material transfer from  hosts to single EhV-163 virions was confirmed by combining stable isotope probing (SIP) experiments with Raman microspectroscopy. Inheritance of the host cells' C-enriched isotopic signature was quantified based on red shifts of Raman peaks characteristic of phenylalanine's phenyl ring. Two-dimensional Raman mapping of EhV-infected  cells revealed that the compact region producing an intense Raman DNA signal (i.e., the nucleus) in healthy  cells becomes diffuse during the first hours of infection. Raman DNA emissions integrated throughout individual cells decreased during the infection cycle. Our observations are consistent with EhV-163 degrading the host's nuclear DNA, scavenging released nucleotides for its own genome replication, and shedding newly-produced virions prior to host lysis  budding.

Raman Microspectroscopy Goes Viral: Infection Dynamics in the Cosmopolitan Microalga, .

Comprehensive methodologies for monitoring microplastics (MPs) in the ocean are critical for accurately assessing abundances across a broad size spectrum, and to document distributions, sources, sinks, temporal trends, and exposure risks for organisms. Discrete 0.5-L water samples from the northeastern-coast of Venezuela (NECV), Pacific-Arctic Ocean (PAO), and Gulf Stream Current (GSC) were analyzed by Raman microspectroscopy to detect MPs not captured by net-tow surveys. Equivalent spherical diameters (ESD) of most MPs were <5 μm, accounting for 68, 83, 86 % of total inventories in NECV, GSC, PAO samples. We did not observe a single MP particle >53 μm ESD. Abundances of MPs in the 0.5-200 μm size fraction were 5-6 orders of magnitude higher than previous surveys that were almost exclusively based on net tow collections of MPs > 300 μm ESD. Abundances of MPs in NECV samples were ~10-fold higher than those from PAO and GSC. The most abundant polymers were polypropylene (PP), polystyrene (PS) and polyethylene terephthalate (PET), consistent with composition of plastic waste generated globally.

From the Caribbean to the Arctic, the most abundant microplastic particles in the ocean have escaped detection.

Endodontic treatment failures remain a significant treatment challenge. Different bacterial combinations are implicated in post-treatment disease.Enterococcus faecalisis often detected in these biofilms. Calcium hydroxide has many limitations, including low flowability, difficult retrieval, high pH, and limited efficacy against E. faecalis. Here we show that these difficulties can be overcome using Calcium Salicylate (CASA) encapsulated in a photo-cross linked, thermo-reversible F127-DMA hydrogel.

Article	Year
Solution structure of duplex DNA containing a β-carba-Fapy-dG lesion. Chemical research in toxicology\| PubMed ID: 22897814	2012
Structure and stability of duplex DNA containing (5'S)-5',8-cyclo-2'-deoxyadenosine: an oxidatively generated lesion repaired by NER. Chemical research in toxicology\| PubMed ID: 22928555	2012
Single-Cell Growth Rates in Photoautotrophic Populations Measured by Stable Isotope Probing and Resonance Raman Microspectrometry. Frontiers in microbiology\| PubMed ID: 28824580	2017
Tear Down the Fluorescent Curtain: A New Fluorescence Suppression Method for Raman Microspectroscopic Analyses. Scientific reports\| PubMed ID: 31673106	2019
Raman Microspectroscopy Goes Viral: Infection Dynamics in the Cosmopolitan Microalga, . Frontiers in microbiology\| PubMed ID: 34795644	2021
From the Caribbean to the Arctic, the most abundant microplastic particles in the ocean have escaped detection. Marine pollution bulletin\| PubMed ID: 38640763	2024
An Innovative Injectable and Retrievable Drug Delivery System for Endodontic Therapy. Journal of endodontics\| PubMed ID: 40816576	2025

Tatiana Zaliznyak

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