Biology subjects

Berggren, M.

Publications and source records attributed to Berggren, M..

3 recordsLinked to original sources

bioRxiv2025

Lithography-free Water Stable Conductive Polymer Nanowires

Free-standing nanowires can gain intracellular access without causing cellular stress or apoptosis. Current approaches to generate nanowires focus on lithographic patterning and inorganic materials (Si, GaAs, Al2O3, etc.) while organic materials are less explored. Use of organic conductive polymers allows for creation of soft mixed ion-electron conducting nanowires. Processing conductive polymers into nanowires is challenging due to the harsh chemicals and processing conditions used. Here, we demonstrate a lithography-free and scalable method to generate all-organic water-stable nanowires composed of conductive polymers. A nanoporous membrane is filled with conductive polymer in solution followed by a cross-linking step to make the polymer water stable. The surface of the membrane is anisotropically etched using a reactive ion etcher to reveal the polymer inside the pores, which extend from the membrane as nanowires. We interface the nanowires with model algal cells and human primary hematopoietic stem and progenitor cells. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/631660v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@bf44b3org.highwire.dtl.DTLVardef@13782baorg.highwire.dtl.DTLVardef@1679366org.highwire.dtl.DTLVardef@fe1677_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Phylogenomic prediction of interaction networks in the presence of gene duplication

Assigning gene function from genome sequences is a rate-limiting step in molecular biology research. A proteins position within an interaction network can potentially provide insights into its molecular mechanisms. Phylogenetic analysis of evolutionary rate covariation (ERC) in protein sequence has been shown to be effective for large-scale prediction of functional relationships and interactions. However, gene duplication, gene loss, and other sources of phylogenetic incongruence are barriers for analyzing ERC on a genome-wide basis. Here, we developed ERCnet, a bioinformatic program designed to overcome these challenges, facilitating efficient all- vs-all ERC analyses for large protein sequence datasets. We simulated proteome datasets and found that ERCnet achieves combined false positive and negative error rates well below 10% and that our novel branch-by-branch length measurements outperforms root-to-tip approaches in most cases, offering a valuable new strategy for performing ERC. We also compiled a sample set of 35 angiosperm genomes to test the performance of ERCnet on empirical data, including its sensitivity to user-defined analysis parameters such as input dataset size and branch-length measurement strategy. We investigated the overlap between ERCnet runs with different species samples to understand how species number and composition affect predicted interactions and to identify the protein sets that consistently exhibit ERC across angiosperms. Our systematic exploration of the performance of ERCnet provides a roadmap for design of future ERC analyses to predict functional interactions in a wide array of genomic datasets. ERCnet code is freely available at https://github.com/EvanForsythe/ERCnet.

genomics↗

bioRxiv2020

A chronic photocapacitor implant for noninvasive neurostimulation with deep red light

Implantable clinical neuroelectronic devices are limited by a lack of reliable, safe, and minimally invasive methods to wirelessly modulate neural tissue. Here, we address this challenge by using organic electrolytic photocapacitors (OEPCs) to perform chronic peripheral nerve stimulation via transduction of tissue-penetrating deep-red light into electrical signals. The operating principle of the OEPC relies on efficient charge generation by nanoscale organic semiconductors comprising nontoxic commercial pigments. OEPCs integrated on an ultrathin cuff are implanted, and light impulses at wavelengths in the tissue transparency window are used to stimulate from outside of the body. Typical stimulation parameters involve irradiation with pulses of 50-1000 s length (638 or 660 nm), capable of actuating the implant about 10 mm below the skin. We detail how to benchmark performance parameters of OEPCs first ex vivo, and in vivo using a rat sciatic nerve. Incorporation of a microfabricated zip-tie mechanism enabled stable, long-term nerve implantation of OEPC devices in rats, with sustained ability to non-invasively mediate neurostimulation over 100 days. OEPC devices introduce a high performance, ultralow volume (0.1 mm3), biocompatible approach to wireless neuromodulation, with potential applicability to an array of clinical bioelectronics.

neuroscience↗