Biology subjects

Bauer, D.

Publications and source records attributed to Bauer, D..

At least 19 recordsLinked to original sources

bioRxiv2025

Machine Learning-Driven Discovery of Synergistic Protein Interactions Identifies ATL3 as a Putative Biomarker for Cancer Drug Response

BackgroundResistance to targeted molecular therapies--both primary and acquired--remains a major obstacle to effective cancer treatment. Despite extensive research, the molecular determinants of treatment resistance are still incompletely understood, underscoring the need to identify robust resistance drivers to improve therapeutic outcomes. Recently, the ProCan and Wellcome Sanger Institute released the worlds largest pan-cancer proteomic dataset to date, comprising 949 cancer cell lines treated with 625 anti-cancer agents. Despite progress in identifying single protein markers, scalable methods for detecting synergistic protein interactions driving drug susceptibility remain limited. Machine learning models such as random forests may offer a robust framework for capturing non-linear protein interactions across diverse cancer types. ResultsOur study presents synerOmics, a scalable framework for identifying putative synergistic protein interactions by leveraging parent-child co-occurrences in random forest regression trees to reduce the interaction search space. We validated our approach using simulated data and two independent cancer proteomic datasets, identifying both pan-cancer and breast cancer-specific markers associated with drug susceptibility. Synergistic interactions that consistently replicated across datasets were enriched for endoplasmic reticulum stress pathways. Notably, shared targets included established sensitivity markers for tyrosine kinase inhibitors (TKIs) and revealed a resistance-associated network centred on ATL3, which demonstrated both prognostic and predictive relevance. ConclusionsApplying synerOmics to the largest cancer cell line proteomic dataset to date, we identified ATL3 as a strong candidate biomarker for lapatinib resistance in breast cancer, with superior predictive performance compared to the current gold standard sensitivity biomarker, ERBB2. HighlightsO_LIWe present a machine learning framework for drug response biomarker discovery, leveraging the largest proteomic cancer cell line dataset, ProCan-DepMapSanger C_LIO_LIATL3 is proposed as a candidate predictive biomarker for lapatinib resistance in breast cancer C_LIO_LIElevated expression of a novel resistance-conferring subcluster centered on ATL3 is associated with poor prognosis across 11 TCGA cancer types C_LIO_LIBaseline drug resistance may be broadly driven by stress pathways, with ER stress and protein ATL3 implicated in ER-phagy in response to TKIs. C_LI

cancer biology↗

bioRxiv2025

Direct and indirect regulation of fetal globin transcript by RNA-binding protein IGF2BP1

Despite extensive investigation, the molecular control of developmental hemoglobin expression remains incompletely elucidated. Hemoglobin switching is controlled by transcription factors, miRNAs, and RNA-binding proteins (RBPs) that enforce gene regulatory changes through development. Here we examine the role of the heterochronically silenced N-6 methyladenosine (m6A) RNA-binding protein IGF2BP1 that was previously described to regulate HBG1/2 indirectly by suppressing BCL11A expression through an unknown mechanism. We find that IGF2BP1 binds and activates HIC2, itself a BCL11A repressor. Furthermore, we identify that IGF2BP1 plays a BCL11A-independent role by direct binding to HBG1/2 to promote its translation. Stop codon-proximal m6A-modified coding sequences within HBG2 transcripts are necessary and sufficient for direct positive regulation mediated by IGF2BP1. This work deepens the mechanistic understanding of hemoglobin switching and suggests a physical relationship between heterochronic RBPs and globin transcripts.

genetics↗

bioRxiv2025

Microenvironmental information significantly improves the recognition of cell types in human lung cancer patients

Accurate single-cell phenotypic classification in histopathological tissue sections is essential for understanding tumor behavior, identifying potential therapeutic targets, and improving prognostic assessments in cancer research. In this study, we applied deep learning to classify lung cancer cell phenotypes in hematoxylin and eosin-stained tissue sections. Using 11 whole slide images from 11 patients, we annotated nearly 20,000 cells into seven distinct phenotypes for training and validation. We used a fisheye transformation technique, which modifies images to mimic fisheye camera effects in order to incorporate cellular microenvironment information to enhance deep learning models. We evaluated its effectiveness on lung cancer tissue sections, optimizing transformation parameters and assessing classification performance through multiple cross-validation strategies. Our results demonstrate that the transformation significantly improves classification accuracy, approaching human level performance, particularly for phenotypes that rely on subtle morphological differences. The approach enhances model generalizability across patient samples, highlighting the importance of integrating spatial context in computational pathology. These findings suggest that incorporating adaptive image transformations can significantly improve automated histopathological analysis, with potential implications for more robust and clinically applicable AI-driven diagnostics.

bioinformatics↗

bioRxiv2025

The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination

Myrothamnus flabellifolia is a dioecious resurrection plant endemic to southern Africa that has become an important model for desiccation tolerance. Here, we present a chromosome-level, haplotype-resolved reference genome for M. flabellifolia alongside transcriptomic profiling across a natural dehydration-rehydration cycle. The 1.28 Gb genome exhibits unusually consistent chromatin architecture with putative holocentric chromosome organization across highly divergent haplotypes. We identified an XY sexual system with a small sex-determining region on chromosome 8. Transcriptomic changes during dehydration varied with the severity of water loss and pointed to early suppression of growth, progressive activation of protective mechanisms, and reversible changes in transcript abundance upon rehydration. Co-expression networks and targeted gene family analyses revealed dynamic regulation of LEA and ELIP genes, with evidence of transcriptome "priming" in hydrated plants, with transcript abundance shifting toward highly disordered proteins during desiccation. Enrichment of ABA and light-responsive cis-regulatory elements in key genes support the existence of conserved stress response pathways. M. flabellifolias rich profile of phenolics and antioxidant genes highlight the overlap between desiccation tolerance and medicinal potential. Together, this study provides foundational resources for understanding the genomic architecture and reproductive biology of M. flabellifolia while offering new insights into the mechanisms of desiccation tolerance.

plant biology↗

bioRxiv2024

Crackling Cloud: an event-driven, cloud-based CRISPR-Cas9 guide RNA design tool

Gene editing has been revolutionised by the CRISPR-Cas9 technology. The versatility and ease-of-use of the technology far exceeds its predecessors, however, the selection of a high-quality guide RNA (gRNA) is critical to directing it to a target site. Selecting gRNA calls upon high-performance algorithms that evaluate nuclease activity at on-target and off-target sites. While there are a suite of programs available, many struggle to analyse the largest genomes, or their predictive accuracy is low. We have previously published a program, named Crackling that is amongst the fastest and most accurate tools available, however, it requires an end-user to have access to a traditional high-performance computing environment. Here, we present an adaptation of Crackling, named Crackling Cloud, that takes advantage of modern serverless cloud technologies that are widely available to anyone, and do not consume resources and incur costs when sitting idle, but can scale to use large volumes of resources when analyses require that. Crackling Cloud is provided as a templated solution using technologies of Amazon Web Services, and is available for free on GitHub under the terms of the BSD 3-clause licence: https://github.com/bmds-lab/Crackling-AWS

bioinformatics↗

bioRxiv2024

RNA methylation controls stress granule formation and function during erythropoiesis

Stress granules (SGs) are crucial in RNA regulation, affecting cell fate and function. SGs contain RNAs, some of which can be methylated. We studied m6A RNA modifications during the human CD34+ HSPCs (hCD34+) differentiating into erythroid cells and found that mRNAs encoding many erythroid-specific proteins had decreased methylation during differentiation. Increased levels ALKBH5 demethylase during erythropoiesis controls the levels of the 3UTR methylation of these mRNAs. hCD34+ carrying ALKBH5 mutations demonstrated a block in erythropoiesis, and mass-spectrometry studies of the mutant cells showed decreased levels of SG proteins, including the core granule protein ATXN2. ALKBH5 directly regulates the methylation of the mRNA of ATXN2. ATXN2 overexpression accelerated the erythroid differentiation of HSPCs and rescued the erythroid differentiation of ALKBH5 mutant cells. Very few SGs are found in normal human erythroid progenitors. SGs accumulated substantially in ALKBH5 mutant cells, and surprisingly overexpression of ATNX2 reduced SG numbers to normal. Polysome analysis demonstrated m6A-modified RNAs to be enriched in the pre-polysome fractions that were less translated. This work establishes a mechanism by which during stress, ATXN2 facilitates the release of SG-stored m6A-modified RNAs including erythroid-specific and SG-enriched RNAs that are loaded onto functional ribosomes, allowing better translation and accelerated erythroid differentiation during stress.

cell biology↗

bioRxiv2024

Targeted Alpha Therapy with Ac-Macropa-Isatuximab for CD38-positive Hematological Malignancies

BackgroundHematological malignancies include diverse cancers related to immune system cells and blood-forming tissue. Treatment resistance and relapse are common despite the introduction of novel therapeutics. Following the development of the PET probe [89Zr]Zr-DFO-isatuximab, targeting the overexpressed CD38 receptor, we developed [225Ac]Ac-Macropa-isatuximab for targeted alpha therapy in murine models of human multiple myeloma (MM) and lymphoma. MethodsIn vitro studies were performed using the CD38 expressing MM1.S (human MM) and Daudi (human lymphoma). Radiopharmaceutical therapy studies were performed in female NSG mice, and the disseminated disease models were established by intravenous injection of luciferase-transfected cells. Mice were randomized (n = 10 mice per cohort) and received a high activity (5.5 kBq) or low activity (2.7 kBq) of [225Ac]Ac-Macropa-Isatuximab in single or multiple cycles. Controls receiving untargeted [225Ac]Ac-Macropa-IgG or saline were included. Tumor burden was measured by bioluminescence imaging (BLI). Weight loss greater than 20% or leg paralysis were used as endpoints. Results[225Ac]Ac-Macropa-Isatuximab was obtained with high radiochemical yield and purity (>95%). It displayed high immunoreactivity and excellent stability in human serum over 10 days. The therapeutic effect of [225Ac]Ac-mcp-Isatuximab was significant for all the treatment cohorts compared to the saline control after administration of the first cycle. Low activities were better tolerated in general, resulting in extended median survivals. The most successful regimen in the MM model was the dual cycle of low activity, with a median survival of 60 days (P < 0.001). In the lymphoma model, the single high activity of 5.5 kBq and four low activity of 2.7 kBq resulted in similar median survivals of 143 days (P < 0.0001) and 147 days (P < 0.0001). These regimens resulted in complete responses with no detectable cancer cells in some cases. Remarkably, no significant kidney damage was observed in any of the models. Conclusion[225Ac]Ac-Macropa-Isatuximab selectively targets CD38, reducing tumor growth and, in some cases, tumor eradication, especially when applied in multiple cycles. Importantly, it has not been associated with significant toxicities at levels of administered activity required for therapeutic benefit, indicating its promise as a therapeutic option.

pharmacology and toxicology↗

bioRxiv2024

CRISPR-CLEAR: Nucleotide-Resolution Mapping of Regulatory Elements via Allelic Readout of Tiled Base Editing

CRISPR tiling screens have advanced the identification and characterization of regulatory sequences but are limited by low resolution arising from the indirect readout of editing via guide RNA sequencing. This study introduces CRISPR-CLEAR, an end-to-end experimental assay and computational pipeline, which leverages targeted sequencing of CRISPR-introduced alleles at the endogenous target locus following dense base-editing mutagenesis. This approach enables the dissection of regulatory elements at nucleotide resolution, facilitating a direct assessment of genotype-phenotype effects.

genomics↗

bioRxiv2024

Wavelet transform of single-trial vestibular short-latency evoked potential reveals temporary reduction in signal detectability and temporal precision following noise exposure

The vestibular short-latency evoked potential (VsEP) reflects the activity of irregular vestibular afferents and their target neurons in the brain stem. Attenuation of trial-averaged VsEP waveforms is widely accepted as an indicator of vestibular dysfunction, however, more quantitative analyses of VsEP waveforms could reveal underlying neural properties of VsEP waveforms. Here, we present a time-frequency analysis of the VsEP with a wavelet transform on a single-trial basis, which allows us to examine trial-by-trial variability in the strength of VsEP waves as well as their temporal coherence across trials. Using this method, we examined changes in the VsEP following 110 dB SPL noise exposure in rats. We found detectability of head jerks based on the power of wavelet transform coefficients was significantly reduced 1 day after noise exposure but recovered nearly to pre-exposure level in 3 - 7 days and completely by 28 days after exposure. Temporal coherence of VsEP waves across trials was also significantly reduced on 1 day after exposure but recovered with a similar time course. Additionally, we found a significant reduction in the number of calretinin-positive calyces in the sacculi collected 28 days after noise exposure. Furthermore, the number of calretinin-positive calyces was significantly correlated with the degree of reduction in temporal coherence and/or signal detectability of the smallest-amplitude jerks. This new analysis of the VsEP provides more quantitative descriptions of noise-induced changes as well as new insights into potential mechanisms underlying noise-induced vestibular dysfunction. Significance StatementOur study presents a new method of VsEP quantification using wavelet transform on a single-trial basis. It also describes a novel approach to determine the stimulus threshold of the VsEP based on signal-detection theory and Rayleigh statistics. The present analysis could also be applied to analysis of auditory brain stem response (ABR). Thus, it has the potential to provide new insights into the physiological properties that underlie peripheral vestibular and auditory dysfunction.

neuroscience↗

bioRxiv2024

Exploring the PET in vivo generator 134Ce as a theranostic match for 225Ac

PurposeThe radionuclide pair cerium-134/lanthanum-134 (134Ce/134La) was recently proposed as a suitable diagnostic counterpart for the therapeutic alpha-emitter actinium-225 (225Ac). The unique properties of 134Ce offer perspectives for developing innovative in vivo investigations not possible with 225Ac. In this work, 225Ac- and 134Ce-labeled tracers were directly compared using internalizing and slow-internalizing cancer models to evaluate their in vivo comparability, progeny meandering, and potential as a matched theranostic pair for clinical translation. Despite being an excellent chemical match, 134Ce/134La has limitations to the setting of quantitative positron emission tomography imaging. MethodsThe precursor PSMA-617 and a macropa-based tetrazine-conjugate (mcp-PEG8-Tz) were radiolabelled with 225Ac or 134Ce and compared in vitro and in vivo using standard (radio)chemical methods. Employing biodistribution studies and positron emission tomography (PET) imaging in athymic nude mice, the radiolabelled PSMA-617 tracers were evaluated in a PC3/PIP (PC3 engineered to express a high level of prostate-specific membrane antigen) prostate cancer mouse model. The 225Ac and 134Ce-labeled mcp-PEG8-Tz were investigated in a BxPC-3 pancreatic tumour model harnessing the pretargeting strategy based on a trans-cyclooctene-modified 5B1 monoclonal antibody. ResultsIn vitro and in vivo studies with both 225Ac and 134Ce-labelled tracers led to comparable results, confirming the matching pharmacokinetics of this theranostic pair. However, PET imaging of the 134Ce-labelled precursors indicated that quantification is highly dependent on tracer internalization due to the redistribution of 134Ces PET-compatible daughter 134La. Consequently, radiotracers based on internalizing vectors like PSMA-617 are suited for this theranostic pair, while slow-internalizing 225Ac-labelled tracers are not quantitatively represented by 134Ce PET imaging. ConclusionWhen employing slow-internalizing vectors, 134Ce might not be an ideal match for 225Ac due to the underestimation of tumour uptake caused by the in vivo redistribution of 134La. However, this same characteristic makes it possible to estimate the redistribution of 225Acs progeny noninvasively. In future studies, this unique PET in vivo generator will further be harnessed to study tracer internalization, trafficking of receptors, and the progression of the tumour microenvironment. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/591165v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@ca3cb6org.highwire.dtl.DTLVardef@157eac6org.highwire.dtl.DTLVardef@f6ac6dorg.highwire.dtl.DTLVardef@b24d87_HPS_FORMAT_FIGEXP M_FIG C_FIG Redistribution of progeny. Investigating the 225Ac and 134Ce decay chain. This figure was created with BioRender.

pharmacology and toxicology↗

bioRxiv2024

Direct delivery of stabilized Cas-embedded base editors achieves efficient and accurate editing of clinically relevant targets

Over the last 5 years, cytosine base editors (CBEs) have emerged as a promising therapeutic tool for specific editing of single nucleotide variants and disrupting specific genes associated with disease. Despite this promise, the currently available CBEs have the significant liabilities of off-target and bystander editing activities, in part due to the mechanism by which they are delivered, causing limitations in their potential applications. In this study we engineeredhighly stabilized Cas-embedded CBEs (sCE_CBEs) that integrate several recent advances, andthat are highly expressible and soluble for direct delivery into cells as ribonucleoprotein (RNP) complexes. Our resulting sCE_CBE RNP complexes efficiently and specifically target TC dinucleotides with minimal off-target or bystander mutations. Additional uracil glycosylase inhibitor (UGI) protein in trans further increased C-to-T editing efficiency and target purity in a dose-dependent manner, minimizing indel formation to untreated levels. A single electroporation was sufficient to effectively edit the therapeutically relevant locus for sickle cell disease in hematopoietic stem and progenitor cells (HSPC) in a dose dependent manner without cellular toxicity. Significantly, these sCE_CBE RNPs permitted for the transplantation of edited HSPCs confirming highly efficient editing in engrafting hematopoietic stem cells in mice. The success of the designed sCBE editors, with improved solubility and enhanced on-target editing, demonstrates promising agents for cytosine base editing at other disease-related sites in HSPCs and other cell types.

biochemistry↗

bioRxiv2024

When the pen is mightier than the sword: semi-automatic 2 and 3D image labelling

Data is the driving engine of learning-based algorithms, the creation of which fundamentally determines the performance, accuracy, generalizability and quality of any model or method trained on it. When only skilled or trained personnel can create reliable annotations, assisted software solutions are desirable to reduce the time and effort the expert must spend on labelling. Herein is proposed an automated annotation helper software package in napari that offers multiple methods to assist the annotator in creating object-based labels on 2D or 3D images.

bioinformatics↗

bioRxiv2023

Noise-induced changes in rat head stability and orientation correlate with dysfunction of otolith irregular afferents

Exposure to intense noise damages both the cochlea and vestibular end organs. Our group previously reported attenuated vestibular short-latency evoked potentials (VsEP) and reduced numbers of calretinin-positive (CR+) calyces in the saccule following noise exposure. Here, we examined rats resting head orientation with respect to gravity as well as head stability following a 4-hour exposure to 120 dB SPL noise. We also assessed how behavioral changes are related to changes in VsEP waveforms and calretinin expression in the utricle and saccule to elucidate potential underlying mechanisms. We found significant reductions in the P2N2 and N2P3 amplitudes following noise exposure. The number of CR+ calyces in both saccule and utricle were also significantly reduced. The size of the reduction in N2P3 amplitude was significantly correlated to the number of CR+ calyces. Animals with a greater loss of CR+ calyces in the utricle following noise showed significant decreases in the average speed of y-axis rotational head motion, while those with a fewer loss of CR+ calyces showed significant increases. In addition, animals with larger noise-induced changes in VsEP and CR+ calyces held their heads motionless longer following noise exposure. We hypothesize that noise exposure is inherently destructive to an animals head stability and thereby manifests as an increase in average head speed in mildly to moderately affected animals. But when the damage was large enough, animals exhibited reduced duration and head motion speed as a behavioral adaptation. The noise exposure also significantly altered the pitch angle of head orientation in animals who had the largest reduction in CR+ calyces in the saccule, suggesting that saccular irregular afferents, including those that are CR+, are critical in control of head and body posture.

neuroscience↗

bioRxiv2023

Evolutionary analyses of gene expression divergence in Panicum hallii: exploring constitutive and plastic responses using reciprocal transplants

The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis-polymorphisms and through more widespread effects driven by trans-regulatory factors. Lovell et al. (2018) studied expression divergence between two ecotypes of Panicum hallii using expression quantitative trait loci (eQTL) analyses and discovered a pre-dominance of cis and several trans-regulatory divergences. Here, we explore expression and sequence divergence in a large sample of P. hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibited genotype-by-site interactions. We used a modified Fst-Qst outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging the earlier eQTL results, we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis-drought interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence (FST, DXY) of promoters and coding sequence of constitutive expression outliers, but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.

evolutionary biology↗

bioRxiv2023

Predicting CRISPR-Cas12a guide efficiency for targeting using Machine Learning

Genome editing through the development of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) - Cas technology has revolutionized many fields in biology. Beyond Cas9 nucleases, Cas12a (formerly Cpf1) has emerged as a promising alternative to Cas9 for editing AT-rich genomes. Despite the promises, guide RNA efficiency prediction through computational tools search still lacks accuracy. Through a computational meta-analysis, here we report that Cas12a target and off-target cleavage behaviour are factor of nucleotide bias combined with nucleotide mismatches relative to the protospacer adjacent motif (PAM) site. These features helped to train a machine learning random forest algorithm to improve the accuracy by at least 15% to existing algorithms to predict guide RNA efficiency for Cas12a enzyme. Despite the progresses, our report underscores the need for more representative datasets and further benchmarking to reliably and accurately predict guide RNA efficiency and off-target effects for Cas12a enzymes.

bioinformatics↗

bioRxiv2023

Radiances of Cerenkov-Emitting Isotopes on the IVIS

Cerenkov (or Cherenkov) luminescence occurs when charged particles exceed the phase velocity of a given medium. Cerenkov has gained interest in preclinical space as well as in clinical trials for optical visualization of numerous radionuclides. However, Cerenkov intensity has to be inferred from alternative databases with energy emission spectra, or theoretical fluence estimates. Here we present the largest experimental dataset of Cerenkov emitting isotopes recorded using the IVIS optical imaging system. We report Cerenkov measurements spanning orders of magnitude normalized to the activity concentration for 21 Cerenkov emitting isotopes, covering electron, alpha, beta minus, and positron emissions. Isotopes measured include Carbon-11, Fluorine-18, Phosphorous-32, Scandium-47, Copper-64, Copper-67, Gallium-68, Arsenic-72, Bromine-76, Yttrium-86, Zirconium-89, Yttrium-90, Iodine-124, Iodine-131, Cerium-134, Lutetium-177, Lead-203, Lead-212, Radium-223, Actinium-225, and Thorium-227. We hope this updating resource will serve as a rank ordering for comparing isotopes for Cerenkov luminescence in the visible window and serve as a rule of thumb for comparing Cerenkov intensities in vitro and in vivo. MethodsAll Cerenkov emitting radionuclides were either produced at Memorial Sloan Kettering Cancer Center (Carbon-11, 11C; Fluorine-18, 18F; Iodine-124, 124I), from commercial sources such as Perkin Elmer (Phosphorous-32, 32P; Yttrium-90, 90Y), Bayer (Radium-223, 223Ra, Xofigo), 3D-Imaging (Zirconium-89, 89Zr), Nuclear Diagnostic Products (Iodine-131, 131I), or from academic collaborators at Washington University at St. Louis (Copper-64, 64Cu), University of Wisconsin (Bromine-76, 76Br), MD Anderson Cancer Center (Yttrium-86, 86Y), Brookhaven National Laboratory (Arsenic-72, 72As; Thorium-227, 227Th), or Oak Ridge National Laboratory (Cerium-134, 134Ce, Actinium-225, 225Ac), and Viewpoint Molecular Targeting (Lead-203, 203Pb; Lead 212, 212Pb). All isotopes were diluted in triplicate on a black bottomed corning 96 well plate to several activity concentrations ranging from 0.1-250 Ci in 100-200 L of Phosphate Buffered Saline. Cerenkov imaging was acquired on a single Perkin-Elmer Spectrum In-Vivo Imaging System (IVIS) at field of view c with exposures ranging up to 15 minutes or lower provided no part of the image intensity was saturated, or that the activity significantly changed during the exposure. Experimental radiances on the IVIS were calculated from regions of interest drown over each 96 well, and then normalized for the activity present in the well, and the volume the isotope was diluted into.

bioengineering↗

bioRxiv2022

Ocean currents drive the worldwide colonization of the most widespread marine plant, eelgrass (Zostera marina)

Currents are unique drivers of oceanic phylogeography and so determine the distribution of marine coastal species, along with past glaciations and sea level changes. Here, we reconstruct the worldwide colonization history of eelgrass (Zostera marina L.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Multiple west to east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival of Z. marina in the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present since [~]208 Kya (thousand years ago). Mediterranean populations were founded [~]53 Kya while extant distributions along western and eastern Atlantic shores coincide with the end of the Last Glacial Maximum ([~]20 Kya). The recent colonization and 5-to 7-fold lower genomic diversity of Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.

evolutionary biology↗

bioRxiv2022

Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi

Colletotrichum fungi infect a wide diversity of monocot and eudicot hosts, causing plant diseases on almost all economically important crops worldwide. In addition to its economic impact, Colletotrichum is a suitable model for the study of gene family evolution on a fine scale to uncover events in the genome that are associated with the evolution of biological characters important for host interactions. Here we present the genome sequences of 30 Colletotrichum species, 18 of them newly sequenced, covering the taxonomic diversity within the genus. A time-calibrated tree revealed that the Colletotrichum ancestor diverged in the late Cretaceous around 70 million years ago (mya) in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from eudicots to monocots during the evolution of this pathogen, coinciding with a progressive shrinking of the degradative arsenal and expansions in lineage specific genes. Comparative transcriptomics of four reference species with different evolutionary histories and adapted to different hosts revealed similarity in gene content but differences in the modulation of their transcription profiles. Only a few orthologs show similar expression profiles on different plant cell walls. Combining genome sequences and expression profiles we identified a set of core genes, such as specific transcription factors, involved in plant cell wall degradation in Colletotrichum.Together, these results indicate that the ancestral Colletotrichum were associated with eudicot plants and certain branches progressively adapted to different monocot hosts, reshaping part of the degradative and transcriptional arsenal.

microbiology↗