Biology subjects

Burger, M.

Publications and source records attributed to Burger, M..

11 recordsLinked to original sources

bioRxiv2026

Untargeted metabolomics reveals host responses and metabolites linked to host compatibility in Rafflesiaceae parasitism

Rafflesiaceae, including Rafflesia, Sapria, and Rhizanthes, are some of the rarest flowering plants in the world, known for producing the largest blooms on Earth. These holoparasites depend exclusively on Tetrastigma (Vitaceae) vines, yet the chemical basis for this host specificity is poorly understood, complicating conservation efforts. Untargeted negative-ion LC- MS metabolomics was used to profile Rafflesiaceae buds and seeds, infected Tetrastigma hosts associated with Rafflesia lagascae, R. speciosa, and Sapria himalayana, uninfected Tetrastigma hosts, and corresponding non-host species from the Philippines and Thailand. Python scripts used for data processing and visualization were developed with generative AI assistance and validated by the authors. Principal component analysis revealed distinct metabolomic profiles across samples, with significant shifts in host metabolites upon infection. Infected Tetrastigma tissues showed nominal enrichment in phenylpropanoid and gibberellin-related metabolites, suggestive of defense and hormonal pathway activation during Rafflesia infection, as well as citric acid, suggesting increased energy demand to support the parasite. Non-host Tetrastigma species showed nominal enrichment in metabolites putatively annotated as stilbenoids, resveratrol diglucosides, and condensed tannins such as procyanidin B2, compounds broadly associated with plant defense. Rafflesia seeds harbored fatty acids/oxylipins, while Rafflesia buds accumulated gallic acid derivatives, compounds also reported in galls. These findings support a chemically mediated model of host compatibility and parasitism, with implications for the ex-situ conservation of these endangered plants.

plant biology↗

bioRxiv2025

Two phytohormones synergistically induce parasitic weeds seed germination via KAI2d receptors

Root parasitic plants can severely decrease global crop production. The germination of their seeds is induced by host root-derived strigolactones (SLs). Considering this unique germination system, a "suicidal germination" method has been proposed to control root parasitic plants. However, this method requires the cost-effective production of germination inducers. In this study, we determined that jasmonates and SLs can synergistically induce the seed germination of root parasitic plants (Orobanche minor and Striga hermonthica). Biochemical analyses indicated that jasmonates and SLs cooperatively activate multiple divergent KARRIKIN INSENSITIVE 2 receptors. Our findings have elucidated the host recognition systems associated with these highly duplicated promiscuous receptors, with potential implications for developing a new strategy to protect crops against root parasitic plants.

plant biology↗

bioRxiv2024

Rapid selection of transgenic mammalian cells via diphtheria toxin resistance

The ability to generate stable transgenic mammalian cell lines is crucial to the investigation of gene functions and the production of recombinant proteins. Currently, mammalian cells can be readily transfected in cell culture settings via both viral and nonviral vectors to induce transgene expression. However, there is an unmet need for efficient selection of transfected cells, since current methods involve rather inefficient antibiotic selection protocols or require the coexpression of fluorescent marker proteins, followed by laborious cell sorting procedures. Our aim was to implement a rapid and efficient in situ selection approach for transgene-expressing human cells, using an engineered diphtheria toxin (DT) resistance-based selection, referred to as selecDT. We demonstrated that selecDT is expressed on the surface of modified human cells, provides efficient protection from DT by inactivating its uptake receptor, and, therefore, enables selection. Current antibiotic-based methods require selection periods of more than a week and often achieve only limited cell enrichment. With selecDT, one day of selection is sufficient to obtain nearly 100% enrichment. The DT resistance described herein may thus positively impact biotechnological processes and biomedical research.

bioengineering↗

bioRxiv2023

Molecular Determinants of Calcitriol Signaling and Sensitivity in Glioma Stem-like Cells

Glioblastoma is the most common primary brain cancer in adults and represents one of the worst cancer diagnosis for the patients. Suffering from a poor prognosis and limited treatment options, tumor recurrences are virtually inevitable. Additionally, treatment resistance is very common for this disease and worsens the prognosis. These and others factors are hypothesized to be largely due to the fact that glioblastoma cells are known to be able to obtain stem-like traits and thereby driving these phenotypes. Recently, we could show that the in vitro and ex vivo treatment of glioblastoma stem-like cells with the hormonally active form of Vitamin D3, Calcitriol (1,25(OH)2-vitamin D3) can block stemness in a subset of cell lines and reduce tumor growth. Here, we expanded our cell panel to over 40 different cultures and can show that, while half of the tested cell lines are sensitive, a quarter can be classified as high-responders. Using genetic and proteomic analysis, we further determined that treatment success can be partially explained by specific polymorphism of the Vitamin D3 receptor and that high-responders display a proteome suggestive of blockade of stemness, as well as migratory potential.

cancer biology↗

bioRxiv2023

A special envelope separates extra-chromosomal from chromosomal DNA in the cytoplasm of mammalian cells

Expression from transfected plasmid DNA is generally transient, but little do we know on what limits this. Live-cell imaging revealed that DNA transfected into mammalian cells was either captured directly in the cytoplasm, or was soon expelled from the nucleus, upon its entry. In the cytoplasm, plasmid DNA was rapidly surrounded by a double membrane and frequently colocalized with extra-chromosomal DNA of telomeric origin, also expelled from the nucleus. Therefore, we termed this long-term maintained structure exclusome. The exclusome envelope contains endoplasmic reticulum proteins, the inner-nuclear membrane proteins Lap2{beta} and Emerin but differs from the nuclear envelope by the absence of the Lamin B Receptor, nuclear pore complexes and by the presence of fenestrations. Further, Emerin affects the frequency of cells with exclusomes. Thus, cells wrap chromosomes and extra-chromosomal DNA into similar yet distinct envelopes. Thereby, they distinguish, sort, cluster, package, and keep extra-chromosomal DNA in the exclusome but chromosomal DNA in the nucleus, where transcription occurs.

cell biology↗

bioRxiv2022

Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

Lymphocytes play a key role in immune surveillance of tumors, but our understanding of the spatial organization and physical interactions that facilitate lymphocyte anti-cancer functions is limited. Here, we used multiplexed imaging, quantitative spatial analysis, and machine learning to create high-definition maps of tumor-bearing lung tissues from a Kras/p53 (KP) mouse model and human resections. Networks of directly interacting lymphocytes ( lymphonets) emerge as a distinctive feature of the anti-cancer immune response. Lymphonets nucleate from small T-cell clusters and incorporate B cells with increasing size. CXCR3-mediated trafficking modulates lymphonet size and number, but neoantigen expression directs intratumoral localization. Lymphonets preferentially harbor TCF1+/PD1+ progenitor CD8 T cells involved in responses to immune checkpoint blockade (ICB). Upon treatment of mice with ICB therapy or a neoantigen-targeted vaccine, lymphonets retain progenitor and gain cytotoxic CD8 T-cell populations, likely via progenitor differentiation. These data show that lymphonets create a spatial environment supportive of CD8 T-cell anti-tumor responses.

cancer biology↗

bioRxiv2022

Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data

New highly-multiplexed imaging technologies have enabled the study of tissues in unprecedented detail. These methods are increasingly being applied to understand how cancer cells and immune response change during tumor development, progression, and metastasis, as well as following treatment. Yet, existing analysis approaches focus on investigating small tissue samples on a per-cell basis, not taking into account the spatial proximity of cells, which indicates cell-cell interaction and specific biological processes in the larger cancer microenvironment. We present Visinity, a scalable visual analytics system to analyze cell interaction patterns across cohorts of whole-slide multiplexed tissue images. Our approach is based on a fast regional neighborhood computation, leveraging unsupervised learning to quantify, compare, and group cells by their surrounding cellular neighborhood. These neighborhoods can be visually analyzed in an exploratory and confirmatory workflow. Users can explore spatial patterns present across tissues through a scalable image viewer and coordinated views highlighting the neighborhood composition and spatial arrangements of cells. To verify or refine existing hypotheses, users can query for specific patterns to determine their presence and statistical significance. Findings can be interactively annotated, ranked, and compared in the form of small multiples. In two case studies with biomedical experts, we demonstrate that Visinity can identify common biological processes within a human tonsil and uncover novel white-blood cell networks and immune-tumor interactions.

cell biology↗

bioRxiv2019

A microparticulate based formulation to protect therapeutic enzymes from proteolytic digestion: phenylalanine ammonia lyase as case study

Phenylketonuria is a genetic disorder affecting the metabolism of phenylalanine (phe) due to a deficiency in the enzyme phenylalanine hydroxylase. This disorder is characterized by an elevated phe blood level, which can lead to severe intellectual disabilities in newborns. The current strategy to prevent these devastating consequences is limited to a life-long phe-free diet, which implies major lifestyle changes and restrictions. Recently, an injectable enzyme replacement therapy, Pegvaliase, has been approved for treating phenylketonuria, but is associated with significant side-effects. In this study a phe-metabolizing system suitable for oral delivery is designed to overcome the need for daily injections. Active phenylalanine ammonia-lyase (PAL), an enzyme that catalyzes phe metabolism, is loaded into mesoporous silica microparticles (MSPs) with pore sizes ranging from 10 to 35 nm. The surface of the MSPs is lined with a semipermeable barrier to allow permeation of phe while blocking digestive enzymes that degrade PAL. The enzymatic activity can be partially preserved in vitro by coating the MSPs with poly(allylamine) and poly(acrylic acid)-bowman birk (protease inhibitor) conjugate. The carrier system presented herein may provide a general approach to overcome gastro-intestinal proteolytic digestion and to deliver active enzymes to the intestinal lumen for prolonged local action.

bioengineering↗

bioRxiv2019

Optical flow analysis reveals that Kinesin-mediated advection impacts on the orientation of microtubules

The orientation of microtubule networks is exploited by motors to deliver cargoes to specific intracellular destinations, and is thus essential for cell polarity and function. Reconstituted in vitro systems have largely contributed to understanding the molecular framework regulating the behavior of microtubule filaments. In cells however, microtubules are exposed to various biomechanical forces that might impact on their orientation, but little is known about it. Oocytes, which display forceful cytoplasmic streaming, are excellent model systems to study the impact of motion forces on cytoskeletons in vivo. Here we implement variational optical flow analysis as a new approach to analyze the polarity of microtubules in the Drosophila oocyte, a cell that displays distinct Kinesin-dependent streaming. After validating the method as robust for describing microtubule orientation from confocal movies, we find that increasing the speed of flows results in aberrant plus end growth direction. Furthermore, we find that in oocytes where Kinesin is unable to induce cytoplasmic streaming, the growth direction of microtubule plus ends is also altered. These findings lead us to propose that cytoplasmic streaming - and thus motion by advection - contributes to the correct orientation of MTs in vivo. Finally, we propose a possible mechanism for a specialised cytoplasmic actin network (the actin mesh) to act as a regulator of flow speeds; to counteract the recruitment of Kinesin to microtubules. HIGHLIGHT SUMMARYCytoskeletal networks do not exist in isolation, but experience crowded and dynamic intracellular environments. However, microtubule-environment interactions are not well understood, and such system-environment interactions are an unresolved question in biology that demands bridging across disciplines. Here we introduce an optical flow motion estimation approach to study microtubule orientation in the Drosophila oocyte, a cell displaying substantial cytoplasmic streaming. We show that microtubule polarity is affected by the regime of these flows, and furthermore, that the presence of flows is necessary for MTs to adopt their proper polarity. With these findings we are contributing to further understanding how microtubules organize in their impacting natural environment.

cell biology↗

bioRxiv2018

Sexual Dichromatism Drives Diversification Within a Major Radiation of African Amphibians

Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across both micro- and macroevolutionary timescales.

evolutionary biology↗

bioRxiv2018

Zika Virus Infection At Different Pregnancy Stages: Anatomopathological Findings, Target Cells And Viral Persistence In Placental Tissues

Zika virus (ZIKV) infection in humans has been associated with congenital malformations and other neurological disorders, such as Guillain-Barre syndrome. The mechanism(s) of ZIKV intrauterine transmission, the cell types involved, the most vulnerable period of pregnancy for severe outcomes from infection and other physiopathological aspects remain unknown. In this study, we analyzed placental samples obtained at the time of delivery from a group of twenty-four women diagnosed with ZIKV infection during the first, second or third trimesters of pregnancy. Villous immaturity was the main histological finding in the placental tissues, although placentas without alterations were also frequently observed. Significant enhancement of the number of syncytial sprouts was observed in the placentas of women infected during the third trimester, indicating the development of placental abnormalities after ZIKV infection. Hyperplasia of Hofbauer cells (HCs) was also observed in these third-trimester placental tissues, and remarkably, HCs were the only ZIKV-positive fetal cells found in the placentas studied that persisted until birth, as revealed by immunohistochemical (IHC) analysis. Thirty-three percent of women infected during pregnancy delivered infants with congenital abnormalities, although no pattern correlating the gestational stage at infection, the IHC positivity of HCs in placental tissues and the presence of congenital malformations at birth was observed. Placental tissue analysis enabled us to confirm maternal ZIKV infection in cases where serum from the acute infection phase was not available, which reinforces the importance of this technique in identifying possible causal factors of birth defects. The results we observed in the samples from naturally infected pregnant women may contribute to the understanding of some aspects of the pathophysiology of ZIKV.

pathology↗