Biology subjects

Maes, L.

Publications and source records attributed to Maes, L..

9 recordsLinked to original sources

bioRxiv2026

Feasibility study of fluid-structure-growth modelling in the context of endogenous tissue restoration

In situ tissue engineering exploits natural inflammatory responses to turn a synthetic vascular graft into a regenerated, functioning, and living vessel through endogenous tissue restoration. Despite promising preclinical results, challenges remain, especially in high-pressure regimes. To better understand the underlying biological processes and predict long-term outcomes of graft implantation, we propose an in silico approach. We account for the solid mechanics of conduit grafts in high and low pressure regimes, the wall shear stresses, and long-term growth and remodeling through two reduced-order fluid-structure-growth models. The first employs an artificial neural network surrogate model to compute the time-averaged wall shear stress at every growth step, whereas the second evaluates a fully-coupled fluid-structure interaction model every 60 time steps. We thoroughly verify both models and confirm acceptable model-form errors, then calibrate them against data from animal experiments. A validation study comparing in silico predictions with unseen animal data of carotid and pulmonary conduit grafts confirms that the model remains reliable up to at least one month of prediction time, hence in the future enabling in silico optimization of short-term endogenous tissue restoration in tissue engineering vascular grafts.

bioengineering↗

bioRxiv2026

The Role of Smooth Muscle Cell Heterogeneity in Cerebral Autoregulation: A Multi-Scale Physics-Based Modeling Study

Background: Cerebral autoregulation stabilizes cerebral blood flow over a range of cerebral perfusion pressures, but the precise shape of the pressure-flow relationship remains debated. The classical triphasic pressure-flow relationship was recently challenged by experiments demonstrating a quadriphasic response, hypothesized to arise from vessel-size-dependent pressure-diameter responses. We tested this hypothesis and investigated whether these size-dependent responses originate from heterogeneity in smooth muscle cell (SMC) abundance, SMC behavior, or neither. Methods: We developed a computational multi-scale physics-based model of cerebral autoregulation linking SMC activity to vessel-scale diameter regulation and organ-scale blood flow. Four scenarios were evaluated: passive vessels, homogeneous SMC abundance and behavior, heterogeneous SMC abundance, and heterogeneous SMC behavior. Predicted pressure-diameter responses and pressure-flow relationships were compared across scenarios and against experimental observations. Results: In contrast to passive vessels, homogeneous SMC activation produced partial flow stabilization, highlighting the key role of SMCs in autoregulation. However, only heterogeneous SMC behavior reproduced the experimentally observed vessel-size-dependent trends in pressure-diameter responses. This scenario also showed the best agreement with the experimental organ-scale pressure-flow relationship (R-squared = 0.93, nRMSE = 5.96%). Conclusion: The model suggests that vessel-size-dependent SMC behavior underlies vessel-size-dependent pressure-diameter responses and shapes the relationship between cerebral perfusion pressure and cerebral blood flow.

bioengineering↗

bioRxiv2024

Cryo-EM structures of the MnmE-MnmG complex reveal large conformational changes and provide new insights into the mechanism of tRNA modification

MnmE and MnmG form a conserved protein complex responsible for the addition of a 5-carboxymethylaminomethyl (cmnm5) group onto the wobble uridine of several tRNAs. Within this complex, both proteins collaborate intensively to catalyze a tRNA modification reaction that involves glycine as a substrate in addition to three different cofactors, with FAD and NADH binding to MnmG and methylenetetrahydrofolate (5,10-CH2-THF) to MnmE. Without structures of the MnmEG complex it remained enigmatic how these substrates and co-factors can be brought together in a concerted manner. Prior SAXS data suggested that the MnmE (2) and MnmG ({beta}2) homodimers can adopt either an 2{beta}2 or 4{beta}2 complex, depending on the nucleotide state of MnmE. Here, we report the cryo-EM structures of the MnmEG complex in the 2{beta}2 and 4{beta}2 oligomeric states. These structures reveal that MnmE undergoes large conformational changes upon interaction with MnmG, resulting in an asymmetric MnmE dimer. In particular, the functionally important C-terminal helix of MnmE relocates from the 5,10-CH2-THF binding pocket of MnmE to the FAD binding pocket of MnmG, thus suggesting a mechanism for the transfer of an activated methylene group from one active site to the other. Together, these findings provide crucial new insights into the MnmEG-catalyzed reaction. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/625835v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@144e41forg.highwire.dtl.DTLVardef@1dce537org.highwire.dtl.DTLVardef@14c9359org.highwire.dtl.DTLVardef@5dec04_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Mechanical Drivers of Glycosaminoglycan Content Changes in Intact and Damaged Human Cartilage

Articular cartilage undergoes significant degeneration during osteoarthritis, currently lacking effective treatments. This study explores mechanical influences on cartilage health using a novel finite element-based mechanoregulatory model, predicting combined degenerative and regenerative responses to mechanical loading. Calibrated and validated through one-week longitudinal ex vivo experiments on intact and damaged cartilage samples, the model underscores the roles of maximum shear strain, fluid velocity, and dissipated energy in driving changes in cartilage glycosaminoglycan (GAG) content. It delineates the distinct regenerative contributions of fluid velocity and dissipated energy, alongside the degenerative contribution of maximum shear strain, to GAG adaptation in both intact and damaged cartilage under physiological mechanical loading. Remarkably, the model predicts increased GAG production even in damaged cartilage, consistent with our in vitro experimental findings. Beyond advancing our understanding of mechanical loadings role in cartilage homeostasis, our model aligns with contemporary ambitions by exploring the potential of in silico trials to optimize mechanical loading in degenerative joint disease, fostering personalized rehabilitation.

bioengineering↗

bioRxiv2023

Long-term hematopoietic stem cells trigger quiescence in Leishmania parasites

Quiescence and posttreatment relapse constitute an important therapeutic constraint across the microbiological spectrum. This study unveils that Leishmania infantum and L. donovani parasites rapidly enter quiescence after an estimated 4-6 divisions in both mouse and human stem cells of the bone marrow but not in macrophages as primary host cells. Quiescent amastigotes display a reduced size and evidence for a rapid evolutionary adaptation response with genetic alterations. We formally demonstrate that acquisition of a quiescent phenotype endows parasites with a capacity to survive antileishmanial treatment. Transition through quiescence also results in an increased cellular infectivity and high transmission capacity through the sand fly vector. Transcriptional profiling of quiescent and non-quiescent metabolic states identified a limited set of 26 upregulated genes that are of particular interest given their predicted involvement as regulators of cell cycle progression and of gene expression at various levels. The differential gene set constitutes a reliable source for the identification of novel markers and potential drivers of quiescence, a metabolic state bestowing parasites the capacity to escape drug treatment.

microbiology↗

bioRxiv2021

Investigating the Role of Chromatin Remodeler FOXA1 in Ferroptotic Cell Death

Ferroptosis is a lipid peroxidation-dependent mechanism of regulated cell death known to suppress tumor proliferation and progression. Although several genetic and protein hallmarks have been identified in ferroptotic cell death, it remains challenging to fully characterize ferroptosis signaling pathways and to find suitable biomarkers. Moreover, changes taking place in the epigenome of ferroptotic cells remain poorly studied. In this context, we aimed to investigate the role of chromatin remodeler forkhead box protein A1 (FOXA1) in RSL3-treated multiple myeloma cells because, similar to ferroptosis, this transcription factor has been associated with changes in the lipid metabolism, DNA damage, and epithelial-to-mesenchymal transition (EMT). RNA sequencing and Western blot analysis revealed that FOXA1 expression is consistently upregulated upon ferroptosis induction in different in vitro and in vivo disease models. In silico motif analysis and transcription factor enrichment analysis further suggested that ferroptosis-mediated FOXA1 expression is orchestrated by specificity protein 1 (Sp1), a transcription factor known to be influenced by lipid peroxidation. Remarkably, FOXA1 upregulation in ferroptotic myeloma cells did not alter hormone signaling or EMT, two key downstream signaling pathways of FOXA1. CUT&RUN genome-wide transcriptional binding site profiling showed that GPX4-inhibition by RSL3 triggered loss of binding of FOXA1 to pericentromeric regions in multiple myeloma cells, suggesting that this transcription factor is possibly involved in genomic instability, DNA damage, or cellular senescence under ferroptotic conditions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/461056v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1fe44acorg.highwire.dtl.DTLVardef@4ea970org.highwire.dtl.DTLVardef@560fd0org.highwire.dtl.DTLVardef@283874_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Miltefosine enhances infectivity of miltefosine-resistant Leishmania infantum by attenuating innate immune recognition

Miltefosine (MIL) is currently the only oral drug available to treat visceral leishmaniasis but its use as first-line monotherapy has been compromised by an increasing treatment failure. Despite the scarce number of resistant clinical isolates, MIL-resistance by mutations in a single aminophospholipid transporter gene can easily be selected in a laboratory environment. These mutations result in a reduced survival in the mammalian host, which can partially be restored by exposure to MIL, suggesting a kind of drug-dependency. To enable a combined study of the infection dynamics and underlying immunological events for differential in vivo survival, firefly luciferase (PpyRE9) / red fluorescent protein (DsRed) double-reporter strains were generated of MIL-resistant (MIL-R) and syngeneic MIL-sensitive (MIL-S) Leishmania infantum. Results in C57Bl/6 and BALB/c mice show that MIL-R parasites induce an increased innate immune response that is characterized by enhanced influx and infection of neutrophils, monocytes and dendritic cells in the liver and elevated serum IFN-{gamma} levels, finally resulting in a less efficient establishment in liver macrophages. The elevated IFN-{gamma} levels were shown to originate from an increased response of hepatic NK and NKT cells to the MIL-R parasites. In addition, we demonstrated that MIL could increase the in vivo fitness of MIL-R parasites by lowering NK and NKT cell activation, leading to a reduced IFN-{gamma} production. These data provide an immunological basis for the MIL-R-associated attenuated phenotype and for the peculiar drug-dependency that may constitute one of the mechanisms of treatment failure. ImportanceRecently, our laboratory demonstrated an in vivo fitness loss of experimentally selected MIL-R parasites in both the sand fly vector and vertebrate host. These findings could explain the scarce number of MIL-R clinical isolates. Surprisingly, MIL-R parasites developed a MIL-dependency which could partially rescue their fitness loss and which may constitute a mechanism of treatment failure. This research aimed to better understand the immunological basis of the attenuated phenotype and the effect of MIL on infectivity traits. Together, this study provides new insights into the complex interplay between the parasite, drug and host and discloses an immune-related mechanism of treatment failure.

microbiology↗

bioRxiv2020

Evaluation of a pan-Leishmania SL-RNA qPCR assay for parasite detection in laboratory-reared and field-collected sand flies and reservoir hosts.

BackgroundIn eco-epidemiological studies, Leishmania detection in vectors and reservoirs is frequently accomplished by high-throughput and sensitive molecular methods that target minicircle kinetoplast DNA (kDNA). A pan-Leishmania SYBR Green quantitative PCR (qPCR) assay which specifically detects the conserved spliced-leader RNA (SL-RNA) sequence has recently been developed. This study comparatively assessed the SL-RNA assay performance for the detection of Leishmania in field and laboratory infected sand flies and in tissue samples from hyraxes as reservoir hosts. Principal findingsThe qPCRs targeting SL-RNA and kDNA performed equally well on infected sand fly samples, despite preservation and extraction under presumed unfavorable conditions for downstream RNA detection. Nucleic acid extraction by a crude extraction buffer combined with a precipitation step was highly compatible with downstream SL-RNA and kDNA detection. Copy numbers of kDNA were found to be identical in culture-derived parasites and promastigotes isolated from sand fly midguts. SL-RNA levels were approximately 3-fold lower in sand fly promastigotes ({Delta}Ct 1.7). The theoretical limit of detection and quantification of the SL-RNA qPCR respectively reached down to 10-3 and 10 parasite equivalents. SL-RNA detection in stored hyrax samples was less efficient with some false negative assay results, most likely due to the long-term tissue storage in absence of RNA stabilizing reagents. ConclusionThis study shows that a crude extraction method in combination with the SL-RNA qPCR assay is suitable for the detection and quantification of Leishmania in sand flies. The assay provides complementary information to the standard kDNA assays, since it is pan-Leishmania specific and detects viable parasites, a prerequisite for identification of vectors and reservoirs. Author summaryIn order to identify vectors and reservoirs of Leishmania, a large number of sand fly and animal tissue samples needs to be screened, because the infection prevalence is generally low. Hence, sensitive low-cost methods are required for nucleic acid isolation and Leishmania detection. Most approaches amplify DNA targets, in particular minicircle kinetoplast DNA (kDNA). Recently, a qPCR was developed that detects the spliced-leader RNA (SL-RNA) sequence, which is conserved among various Leishmania species and allows detection of viable parasites. We show that the SL-RNA qPCR is highly compatible with a low-cost, crude extraction approach and performs equally well on laboratory and field infected sand fly samples as kDNA qPCR assays. The assay can detect 10-3 parasite equivalent in sand flies and enables Leishmania quantification down to 10 parasites. We found that the copy number of SL-RNA is 3-fold lower in sand fly derived promastigotes compared to cultured promastigotes. SL-RNA detection in hyrax tissue samples appeared less efficient, which is presumably due to long-term storage without RNA stabilizing reagents. Overall, our assay is complementary to kDNA assays as it can identify viable Leishmania stages, which provides pivotal information for identification of reservoirs and vectors and their transmission capacity.

microbiology↗

bioRxiv2019

Feeding behavior and activity of Phlebotomus pedifer and potential reservoir hosts of Leishmania aethiopica in southwestern Ethiopia.

BackgroundCutaneous leishmaniasis (CL) is a major public health concern in Ethiopia. However, knowledge about the complex zoonotic transmission cycle is limited, hampering implementation of control strategies. We explored the feeding behavior and activity of the vector (Phlebotomus pedifer) and established the role of livestock in CL transmission. MethodsBlood meal origins of engorged sand flies were determined by sequencing host DNA. A host choice experiment was performed to assess the feeding preference of P. pedifer when humans and hyraxes are equally accessible. Ear and nose biopsies from goats and bovines were screened for the presence of Leishmania parasites. Sand flies were captured indoor and outdoor with human landing catches (HLC) and CDC light traps to determine at which time and where P. pedifer is mostly active. Principal findingsA total of 180 sand flies were found to bite hosts of 12 genera. Humans were the predominant blood meal source (59.4%, p < 0.001) in all habitats, even in caves, where hyraxes are abundant. Only 10.6% of the sand flies fed on hyraxes based on the blood meal analysis, but the host choice experiment revealed that sand flies have a significant preference for feeding on hyraxes over humans (p = 0.009) when hosts are equally accessible. Only a single goat nose biopsy from 412 animal samples was found with Leishmania RNA. We found that P. pedifer is predominantly endophagic (p = 0.003), but occurs both indoors and outdoors. A substantial amount of sand flies was active in the early evening, which increased over time reaching its maximum around midnight. ConclusionWe indicate that Leishmania transmission in southwestern Ethiopia is, in contrast to earlier suggestions, likely mainly anthroponotic and that livestock does not play a role in transmission. Combined indoor and outdoor vector control measures at night are required for efficient vector control. Author summaryCutaneous leishmaniasis is a major public health problem in Ethiopia. It is caused by Leishmania aethiopica protozoa that are transmitted when female sand flies take a blood meal. Hyraxes are assigned as the reservoirs of the infection, because many were found infected with Leishmania. There is very limited knowledge about the behavior of sand flies and other potential hosts of the infection. However, this information is a prerequisite for disease control, which is currently hampered. In this study, we found that humans are likely the main source of the infection and that the role of hyraxes in disease transmission needs further investigation to decide whether they should be included in control programs. Livestock appears not play a role in transmission, even though sand flies like to feed on them. We also show that sand flies are active indoors and outdoors, but have a preference for feeding inside human dwellings and that they are mostly active around midnight. Overall, we conclude that disease prevention and control should emphasize on human protection by applying vector control indoors, at night.

ecology↗