Biology subjects

Graf, T.

Publications and source records attributed to Graf, T..

15 recordsLinked to original sources

bioRxiv2025

Mechanisms and Safety of Ultrasound Phacoemulsification

ObjectiveA comprehensive technical and biomedical analysis of ultrasound-induced effects during phacoemulsification cataract surgery (PCS) and an assessment of the potential risks associated with ultrasound emulsification MethodsModeling ultrasound wave propagation and intensities using the finite element method (FEM). Cavitation onset was experimentally validated in a pressure chamber observed with a high-speed camera. The thermal effects of ultrasound energy were estimated through established physical and thermal models and confirmed in a cuvette setup using thermistor probes. ResultsAt the distal end of the PCS tip, the ultrasound wave intensity reached 0.2 W/mm2, resulting in ocular tissue displacements in the anterior chamber below 2 {micro}m. The temperature rise in the anterior chamber was less than 0.2 {degrees}C/s. Both observations indicate negligible mechanical and thermal risk to ocular tissues. High-speed imaging confirmed cavitation confined to the tip region. Emulsification efficacy was maintained even under conditions that suppressed cavitation, including elevated ambient pressures and cavitation-inhibiting fluids. Results indicate that mechanical fragmentation by tip oscillation ("jackhammer effect") is the only relevant emulsification mechanism, while cavitation plays a negligible role. Acoustic streaming was observed during ultrasound excitation without phaco sleeve. During phacoemulsification, the sleeve suppressed acoustic streaming into the anterior chamber. ConclusionsThe findings validate the safety of ultrasound-based PCS and confirm that tissue fragmentation is primarily driven by the oscillating tips direct action.

bioengineering↗

bioRxiv2024

Synergistic and antagonistic activities of IRF8 and FOS enhancer pairs during an immune cell fate switch

Cell-fate instructive genes tend to be regulated by large clusters of enhancers. Whether and how individual enhancers within such clusters cooperate in regulating gene expression is poorly understood. We have previously developed a computational method, SEGCOND, that identifies hubs consisting of enhancer clusters and their target genes, termed Putative Transcriptional Condensates (PTCs). Using SEGCOND, we identified PTCs in a CEBPA-induced B-cell to macrophage transdifferentiation system. We found them to be enriched for highly expressed, lineage-restricted genes and to associate with BRD4, a component of transcriptional condensates. Here we performed single and combinatorial deletions of enhancers within two active PTCs after transdifferentiation is induced, harboring IRF8 and FOS. Two enhancers within the IRF8 PTC were found to form a backup mechanism when combined, safeguarding IRF8 expression and transdifferentiation kinetics. Unexpectedly, two individual enhancers within the FOS PTC antagonize each other at Day 1 of transdifferentiation, delaying the conversion of B-cells to macrophages and reducing FOS expression, but cooperate to increase FOS levels in Day 7 induced cells. Our results reveal differentiation stage-specific, complex interactions, between individual enhancers within a cluster.

genomics↗

bioRxiv2024

A Laboratory-Adapted and a Clinical Isolate of Dengue Virus Serotype 4 Differently Impact Aedes aegypti Life-History Traits Relevant to Vectorial Capacity

1Dengue virus cases are on the rise globally, and strategies to reduce new infections by controlling its primary vector, the mosquito Aedes aegypti, represent a promising biotechnological approach. However, the interaction between virus serotypes and genotypes with Aedes aegypti is poorly characterized at the molecular level, as well as in terms of life-history traits related to vector capacity and mosquito disease tolerance. Here, we infected Aedes aegypti with two philogenetically distant strains of Dengue virus serotype 4 genotype II: a laboratory-adapted strain, DENV4 - TVP/360, and a recent clinical strain isolated from southern Brazil, DENV4 - LRV 13/422. These strains, which exhibit 26 amino acid differences in their sequences, have been shown in to produce distinct immune phenotypes in vertebrate cells. Here, we assessed various life-history traits of Aedes aegypti, including mortality, fecundity, fertility, and induced flight capacity, as well as vector competence-related parameters such as infection intensity and prevalence, following exposure to different viral concentrations. We found that each viral strain differentially affected mosquito traits. While neither strain significantly reduced mosquito lifespan, Aedes aegypti infection prevalence was influenced by the initial dose of DENV4 - TVP/360. This laboratory-adapted strain also enhanced mosquito induced-flight capacity at early (24 hours post-infection - DPI) and late (21 DPI) time points. On the other hand, the recent clinical isolate, DENV4 - LRV 13/422, specifically reduced Aedes aegypti fertility. A better understanding of how different arbovirus strains influence mosquito life-history traits connected to disease spread will be critical in public health efforts to mitigate arbovirus outbreaks that are focused on the mosquito vector. 2 Highlights- The DENV4 strains TVP/360 and LRV 13/422 have 26 amino acid differences in their sequences. - Aedes aegypti infection prevalence is influenced by the initial dose of DENV4 - TVP/360 strain but not DENV4 - LRV 13/422. - Fertility is specifically reduced by DENV4 - LRV 13/422. - Induced-flight activity is enhanced at 1 and 21 days post-infection with DENV4 - TVP/360 strain.

microbiology↗

bioRxiv2022

The BNT162b2 mRNA SARS-CoV-2 vaccine induces transient afucosylatedIgG1 in naive but not antigen-experienced vaccinees

The onset of severe SARS-CoV-2 infection is characterized by the presence of afucosylated IgG1 responses against the viral spike (S) protein, which can trigger exacerbated inflammatory responses. Here, we studied IgG glycosylation after BNT162b2 SARS-CoV-2 mRNA vaccination to explore whether vaccine-induced S protein expression on host cells also generates afucosylated IgG1 responses. SARS-CoV-2 naive individuals initially showed a transient afucosylated anti-S IgG1 response after the first dose, albeit to a lower extent than severely ill COVID-19 patients. In contrast, previously infected, antigen-experienced individuals had low afucosylation levels, which slightly increased after immunization. Afucosylation levels after the first dose correlated with low fucosyltransferase 8 (FUT8) expression levels in a defined plasma cell subset. Remarkably, IgG afucosylation levels after primary vaccination correlated significantly with IgG levels after the second dose. Further studies are needed to assess efficacy, inflammatory potential, and protective capacity of afucosylated IgG responses. One sentence summaryA transient afucosylated IgG response to the BNT162b2 mRNA vaccine was observed in naive but not in antigen-experienced individuals, which predicted antibody titers upon the second dose.

immunology↗

bioRxiv2022

The RNA-Binding Protein SAM68 regulates cardiomyocyte differentiation by enhancing Gata4 translation

The signal transduction and activation of RNA (STAR) family is composed of RNA-binding proteins (RBPs) that play a central role in mammalian development. Nonetheless, the functions and modes of action that STAR proteins have in lineage specification are still poorly understood. Here, we characterized the role of STAR proteins SAM68 and QUAKING (QKI) in pluripotency and differentiation by performing their depletion through CRISPR-Cas9 in mouse embryonic stem cells (mESCs). Combining RNA-sequencing, ribosome profiling and advanced computational predictions, we found that both SAM68 and QKI regulate the mESCs self-renewal and are indispensable for cardiomyocyte differentiation. At the molecular level, we discovered that SAM68 and QKI antagonistically control the expression of cardiogenic factors. Our calculations indicated that SAM68, unlike QKI, binds the cardiogenic-specific transcription factor Gata4 in a region spanning nucleotides 500 to 1000 of the mRNA corresponding to part of the 5 untranslated region and the first exon. We validated the predictions by electrophoretic mobility shift assay and RNA immunoprecipitation showing that SAM68 controls the translation of Gata4 during mESCs differentiation towards the cardiomyocyte lineage.

molecular biology↗

bioRxiv2021

A potential SARS-CoV-2 variant of interest (VOI) harboring mutation E484K in the Spike protein was identified within lineage B.1.1.33 circulating in Brazil

The SARS-CoV-2 epidemic in Brazil was dominated by two lineages designated as B.1.1.28 and B.1.1.33. Two SARS-CoV-2 variants harboring mutations at the receptor-binding domain of the Spike (S) protein, designated as lineages P.1 and P.2, evolved within lineage B.1.1.28 and are rapidly spreading in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. The VOI N.9 probably emerged in August 2020 and has spread across different Brazilian states from the Southeast, South, North and Northeast regions.

microbiology↗

bioRxiv2020

Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1 and TIA1

In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for cell reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we have studied the dynamics of alternative splicing (AS) changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem (iPS) cells. These changes, generally uncoupled from transcriptional regulation, significantly overlapped with splicing programs reported during reprogramming of mouse embryonic fibroblasts (MEFs). Correlation between gene expression of potential regulators and specific clusters of AS changes enabled the identification and subsequent validation of CPSF3 and hnRNP UL1 as facilitators, and TIA1 as repressor of MEFs reprogramming. These RNA-binding proteins control partially overlapping programs of splicing regulation affecting genes involved in developmental and morphogenetic processes. Our results reveal common programs of splicing regulation during reprogramming of different cell types and identify three novel regulators of this process.

molecular biology↗

bioRxiv2020

β-catenin dependent axial patterning in Cnidaria and Bilateria uses similar regulatory logic

In animals, body axis patterning is based on the concentration-dependent interpretation of graded morphogen signals, which enables correct positioning of the anatomical structures. The most ancient axis patterning system acting across animal phyla relies on {beta}-catenin signaling, which directs gastrulation, and patterns the main body axis. However, within Bilateria, the patterning logic varies significantly between protostomes and deuterostomes. To deduce the ancestral principles of {beta}-catenin dependent axial patterning, we investigated the oral-aboral axis patterning in the sea anemone Nematostella - a member of the bilaterian sister group Cnidaria. Here we elucidate the regulatory logic by which more orally expressed {beta}-catenin targets repress more aborally expressed {beta}- catenin targets, and progressively restrict the initially global, maternally provided aboral identity. Similar regulatory logic of {beta}-catenin-dependent patterning in Nematostella and deuterostomes suggests a common evolutionary origin of these processes.

developmental biology↗

bioRxiv2020

Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil

Despite all efforts to control the COVID-19 spread, the SARS-CoV-2 reached South America within three months after its first detection in China, and Brazil became one of the hotspots of COVID-19 in the world. Several SARS-CoV-2 lineages have been identified and some local clusters have been described in this early pandemic phase in Western countries. Here we investigated the genetic diversity of SARS-CoV-2 during the early phase (late February to late April) of the epidemic in Brazil. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. This SARS-CoV-2 Brazilian lineage was probably established during February 2020 and rapidly spread through the country, reaching different Brazilian regions by the middle of March 2020. Our study also supports occasional exportations of this Brazilian B.1.1 lineage to neighboring South American countries and to more distant countries before the implementation of international air travels restrictions in Brazil.

evolutionary biology↗

bioRxiv2019

RAS mutations drive proliferative chronic myelomonocytic leukemia via activation of a novel KMT2A-PLK1 axis

ABSTRACTChronic myelomonocytic leukemia (CMML) is an aggressive hematological malignancy with limited treatment options. Whole exome (WES) and targeted sequencing of several independent cohorts of CMML patients, comparing dysplastic (dCMML) to proliferative (pCMML) CMML, as well as paired chronic phase disease and acute leukemic transformation (LT), associate acquisition of oncogenic RAS pathway mutations, the most common being NRASG12D, with aggressive disease and with disease progression. Using patient derived progenitor colony assays and a NRASG12D-Vav-Cre mouse model, we further demonstrate the role of mutant RAS signaling in driving and maintaining pCMML phenotype. RNA-sequencing links RAS pathway mutations with an increased expression of genes encoding the mitotic checkpoint kinases PLK1 and WEE1. Further, we dmeoinstrated that non-mutated lysine methyltransferase KMT2A (MLL1) acts as mediator of NRAS-induced PLK1 and WEE1 expression. Finally, we demonstrate the translational value of our findings by showing that pharmacological PLK1 inhibition decreases monocytosis and hepatosplenomegaly while improving hematopoiesis in RAS mutant patient-derived xenografts. Hence, we define severe CMML as oncogenic RAS pathway-enriched malignancies, with a unique gene expression profile regulated by KMT2A, amenable to therapeutic intervention.

cancer biology↗

bioRxiv2019

Dynamic simulations of transcriptional control during cell reprogramming reveal spatial chromatin caging

Chromosome structure is a crucial regulatory factor for a wide range of nuclear processes. Chromosome Conformation Capture (3C)-based experiments combined with computational modelling are pivotal for unveiling 3D chromosome structure. Here, we introduce TADdyn, a new tool that integrates time-course 3C data, restraint-based modelling, and molecular dynamics to simulate the structural rearrangements of genomic loci in a completely data-driven way. We applied TADdyn on in-situ Hi-C time-course experiments studying the reprogramming of murine B cells to pluripotent cells, and characterized the structural rearrangements that take place upon changes in the transcriptional state of 11 genomic loci. TADdyn simulations show that structural cages form around the transcription starting site of active loci to stabilize their dynamics, by initiating (hit) and maintaining (stick) interactions with regulatory regions. Consistent findings with TADdyn for all loci under study suggest that this hit-and-stick mechanism may represent a general mechanism to trigger and stabilize transcription.

bioinformatics↗

bioRxiv2018

Single cell expression analysis uncouples transdifferentiation and reprogramming

Many somatic cell types are plastic, having the capacity to convert into other specialized cells (transdifferentiation)(1) or into induced pluripotent stem cells (iPSCs, reprogramming)(2) in response to transcription factor over-expression. To explore what makes a cell plastic and whether these different cell conversion processes are coupled, we exposed bone marrow derived pre-B cells to two different transcription factor overexpression protocols that efficiently convert them either into macrophages or iPSCs and monitored the two processes over time using single cell gene expression analysis. We found that even in these highly efficient cell fate conversion systems, cells differ in both their speed and path of transdifferentiation and reprogramming. This heterogeneity originatesin two starting pre-B cell subpopulations,large pre-BII and the small pre-BII cells they normally differentiate into. The large cells transdifferentiate slowly but exhibit a high efficiency of iPSC reprogramming. In contrast, the small cells transdifferentiate rapidly but are highly resistant to reprogramming. Moreover, the large B cells induce a stronger transient granulocyte/macrophage progenitor (GMP)-like state, while the small B cells undergo a more direct conversion to the macrophage fate. The large cells are cycling and exhibit high Myc activity whereas the small cells are Myc low and mostly quiescent. The observed heterogeneity of the two cell conversion processes can therefore be traced to two closely related cell types in the starting population that exhibit different types of plasticity. These data show that a somatic cells propensity for either transdifferentiation and reprogramming can be uncoupled.\n\nOne sentence summarySingle cell transcriptomics of cell conversions

developmental biology↗

bioRxiv2017

OneD: increasing reproducibility of Hi-C Samples with abnormal karyotypes

The three-dimensional conformation of genomes is an essential component of their biological activity. The advent of the Hi-C technology enabled an unprecedented progress in our understanding of genome structures. However, Hi-C is subject to systematic biases that can compromise downstream analyses. Several strategies have been proposed to remove those biases, but the issue of abnormal karyotypes received little attention. Many experiments are performed in cancer cell lines, which typically harbor large-scale copy number variations that create visible defects on the raw Hi-C maps. The consequences of these widespread artifacts on the normalized maps are mostly unexplored. We observed that current normalization methods are not robust to the presence of large-scale copy number variations, potentially obscuring biological differences and enhancing batch effects. To address this issue, we developed an alternative approach designed to take into account chromosomal abnormalities. The method, called OneD, increases reproducibility among replicates of Hi-C samples with abnormal karyotype, outperforming previous methods significantly. On normal karyotypes, OneD fared equally well as state-of-the-art methods, making it a safe choice for Hi-C normalization. OneD is fast and scales well in terms of computing resources for resolutions up to 1 kbp. OneD is implemented as an R package available at http://www.github.com/qenvio/dryhic.

bioinformatics↗

bioRxiv2017

Managing The Analysis Of High-Throughput Sequencing Data

T47D_rep2 and b1913e6c1_51720e9cf were two Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high throughput sequencing data.

bioinformatics↗

bioRxiv2017

Transcription Factors Orchestrate Dynamic Interplay Between Genome Topology And Gene Regulation During Cell Reprogramming

Chromosomal architecture is known to influence gene expression, yet its role in controlling cell fate remains poorly understood. Reprogramming of somatic cells into pluripotent stem cells by the transcription factors (TFs) Oct4, Sox2, Klf4 and Myc offers an opportunity to address this question but is severely limited by the low proportion of responding cells. We recently developed a highly efficient reprogramming protocol that synchronously converts somatic into pluripotent stem cells. Here, we employ this system to integrate time-resolved changes in genome topology with gene expression, TF binding and chromatin state dynamics. This revealed that TFs drive topological genome reorganization at multiple architectural levels, which often precedes changes in gene expression. Removal of locus-specific topological barriers can explain why pluripotency genes are activated sequentially, instead of simultaneously, during reprogramming. Taken together, our study implicates genome topology as an instructive force for implementing transcriptional programs and cell fate in mammals.

molecular biology↗