Biology subjects

Zaiss, M.

Publications and source records attributed to Zaiss, M..

4 recordsLinked to original sources

bioRxiv2025

Generalization of Optimal Control Saturation Pulse Design for Robust and High CEST Contrast

PurposeOptimal Control (OC) CEST pulse design for singular pulses that can be used flexibly and robustly with high saturation at different duty cycles, saturation durations and magnetic field strengths. Theory and MethodsAn OC framework was developed to design a single pulse shape that can be flexibly applied for arbitrary pulse train parameters and outperform typically used CEST saturation pulses shapes. The pulse design was developed primarily with a continuous wave spectrum (CW) as the optimization target, but can be easily adapted to specific scenarios. The generalized OC pulse was evaluated through simulations, phantom, and in vivo measurements on a 3 T clinical scanner. Performance was assessed in terms of contrast, robustness to field inhomogeneities, and resilience against artifacts such as Rabi oscillations and sidebands, compared to established saturation techniques. ResultsInvestigations showed that the generalized OC pulse achieved a contrast matching CW saturation and also functioned well under field inhomogeneities. Low-pass filtering of the optimized pulse shape effectively suppressed artifacts outside the initial optimization frequency range, enabling generalization across different field strengths. Phantom experiments consistently showed higher contrast than Gaussian, Fermi, and adiabatic spin-lock pulses for various CEST agents covering most clinically relevant regimes. In vivo imaging demonstrated substantially enhanced CEST contrast for both creatine/phosphocreatine in muscle and Amide Proton Transfer (APT) in brain compared to Gaussian saturation. ConclusionThe generalized OC pulse provides a robust and flexible alternative to conventional CEST saturation strategies. Its integration into the open-source Pulseq-CEST framework supports simple reproducibility and a vendor-independent implementation.

biophysics↗

bioRxiv2025

CRYO-CEST: Non-invasive imaging of cryoprotectants using chemical exchange saturation transfer

Chemical exchange saturation transfer (CEST) MRI at 7T was explored as a non-invasive method to detect and quantify common cryoprotectants used in organ cryopreservation. Phantom experiments demonstrated clear CEST signals from ethylene glycol, formamide, and dimethyl sulfoxide, with formamide showing the most sensitive concentration-dependent response. CEST imaging could thus provide a practical tool for monitoring cryoprotectant concentrations in organs.

biophysics↗

bioRxiv2020

AI boosted molecular MRI for apoptosis detection in oncolytic virotherapy

Oncolytic virotherapy is a promising treatment for high mortality cancers1. Non-invasive imaging of the underlying molecular processes is an essential tool for therapy optimization and assessment of viral spread, innate immunity, and therapeutic response2, 3. However, previous methods for imaging oncolytic viruses did not correlate with late viral activity4 or had poor sensitivity and specificity5. Similarly, methods developed to image treatment response, such as apoptosis, proved to be slow, nonspecific, or require the use of radioactive or metal-based contrast agents6-8. To date, no method has been widely adopted for clinical use. We describe here a new method for fast magnetic resonance molecular imaging with quantitative proton chemical-exchange specificity to monitor oncolytic virotherapy treatment response. A deep neural network enabled the computation of quantitative biomarker maps of protein and lipid/macromolecule concentrations as well as intracellular pH in a glioblastoma multiforme mouse brain tumor model. Early detection of apoptotic response to oncolytic virotherapy, characterized by decreased cytosolic pH and protein synthesis, was observed in agreement with histology. Clinical translation was demonstrated in a normal human subject, yielding molecular parameters in good agreement with literature values9. The developed method is directly applicable to a wide range of pathologies, including stroke10, cancer11-13, and neurological disorders14, 15.

biophysics↗

bioRxiv2019

Infection with a small intestinal helminth Heligmosomoides polygyrus bakeri consistently alters microbial communities throughout the small and large intestine

Increasing evidence suggests that intestinal helminth infection can alter intestinal microbial communities with important impacts on the mammalian host. However, all of the studies to date utilize different techniques to study the microbiome and access different sites of the intestine with little consistency noted between studies. In the present study, we set out to perform a comprehensive analysis of the impact of intestinal helminth infection on the mammalian intestinal bacterial microbiome. For this purpose, we investigated the impact of experimental infection using the natural murine small intestinal helminth, Heligmosomoides polygyrus bakeri (Hpb) and examined possible alterations in both the mucous and luminal bacterial communities along the entire small and large intestine. We also explored the impact of common experimental variables, including the parasite batch and pre-infection microbiome, on the outcome of helminth-bacterial interactions. This work provides evidence that helminth infection reproducibly alters intestinal microbial communities - with an impact of infection noted along the entire length of the intestine. Although the exact nature of helminth-induced alterations to the intestinal microbiome differed depending on the parasite batch and microbiome community structure present prior to infection, changes extended well beyond the introduction of new bacterial species by the infecting larvae. Moreover, striking similarities between different experiments were noted, including the consistent outgrowth of a bacterium belonging to the Peptostreptococcaceae family throughout the intestine.\n\nAuthor SummaryIncreasing evidence indicates a role for interactions between intestinal helminths and the microbiome in regulating mammalian health, and a greater understanding of helminth-microbiota interactions may open the path for the development of novel immunomodulatory therapies. However, such studies are hampered by the inconsistent nature of the data reported so far. Such inconsistancies likely result from variations in the experimental and technological methodologies employed to investigate helminth-microbiota interactions and well has natural variation in the starting microbiome composition and/or worm genetics. We conducted a thorough study in which the reproducibility of helminth-induced alterations of microbial communities was determined and impact of common experimental variables - such as the starting microbiome and parasite batch - was determined. Our work reveals the robust ability of small intestinal helminth infection to alter microbial communities along the entire length of the intestine and additionally identifies a single bacterium that is strongly associated with infection across multiple experiments.

microbiology↗