Biology subjects

Koch, T.

Publications and source records attributed to Koch, T..

10 recordsLinked to original sources

bioRxiv2025

Microbial community analyses of composts are influenced by particle size fraction and DNA extraction method

Composting plays a key role in sustainable agriculture by converting organic waste into a valuable soil conditioner. The process is driven by complex microbial communities, whose characterization is essential for optimizing the composting process and compost quality. Molecular techniques such as amplicon sequencing are commonly used for this purpose. However, sampling procedures and DNA extraction methods, key steps in the sequencing workflow, vary often across studies, challenging comparability. We investigated two aspects of sampling preparation that may influence compost microbial analyses. For DNA extraction, often fine fractions (<2 mm) are used. However, compost has a heterogeneous structure, including coarse particles. To assess the effect of particle size, we separately sequenced bacterial and fungal communities of the fine (0-2 mm) and coarse (2-10 mm) fractions of three composts. In addition, DNA was extracted using a carboxyl affinity-based magnetic method and a silanol affinity-based filter method to evaluate the impact of the extraction technique. We found that the coarse fraction had higher bacterial richness and a distinct bacterial and fungal community structure compared to the fine fraction. DNA extraction method also influenced bacterial community profiles, with the magnetic bead method improving coverage, particularly for Bacillota. Although the effects of particle size and extraction method were small compared to general diversity among composts, we recommend including coarse particles in sequencing analyses and using standardized DNA extraction protocols, especially for studies aiming at high-resolution community analyses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/682543v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1cd1b77org.highwire.dtl.DTLVardef@c64c9corg.highwire.dtl.DTLVardef@cfb5f6org.highwire.dtl.DTLVardef@b350df_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Rational Design and Optimization of a Potent IDO1 Proteolysis Targeting Chimera (PROTAC)

Indoleamine 2,3-dioxygenase 1 (IDO1) is a potently immunosuppressive protein that inhibits antitumor immunity through both tryptophan metabolism and non-enzymatic functions. Pharmacological therapies targeting IDO1 enzyme activity have generally failed to improve the overall survival of patients with cancer. Developing new therapeutic agents that are capable of neutralizing both enzyme-and non-enzyme-derived immunosuppressive IDO1 effects is therefore of high interest. We previously described the development of a novel Proteolysis Targeting Chimera (PROTAC), NU223612, that degrades IDO1 in cultured human glioblastoma (GBM) cells, as well as in well-established brain tumors, in vivo. In this study, we rationally optimized the composition, rigidity, and linker orientation of the PROTAC structure to create NU227326, which degrades IDO1 with a DC50 of 5 nM in human GBM cells. Mechanistic studies showed that IDO1 degradation occurred through the ubiquitin-proteasome system and was sustained for at least 2 days, supporting NU227326 as a highly potent IDO1 PROTAC suitable for further studies in GBM and other human cancers.

biochemistry↗

bioRxiv2024

Estimation of fluid flow velocities in cortical brain tissue driven by the microvasculature

We present a modelling framework for describing bulk fluid flow in brain tissue. Within this framework, using computational simulation, we estimate bulk flow velocities in the gray matter parenchyma due to static or slowly varying water potential gradients--hydrostatic pressure gradients and osmotic pressure gradients. Working with the situation that experimental evidence and some model parameter estimates, as we point out, are presently insufficient to estimate velocities precisely, we explore feasible parameter ranges resulting in a range of estimates. We consider the effect of realistic microvascular architecture (extracted from mouse cortical gray matter). Although the estimated velocities are small in magnitude (e.g. in comparison to blood flow velocities), the passive transport of solutes with the bulk fluid can be a relevant process when considering larger molecules transported over larger distances. We compare velocity magnitudes resulting from filtration and pulsations. Filtration can lead to continuous directed fluid flow in the parenchyma, while pulsation-driven flow is (at least partly) reversible. For the first time, we consider the effect of the vascular architecture on the velocity distribution in a tissue sample of ca. 1 mm3 cortical gray matter tissue. We conclude that both filtration and pulsations are potentially potent drivers for fluid flow. Summary (lay abstract)Fluid transport through brain tissue is dynamic, but the basic properties of this flow and its variability are poorly characterised. Disturbed fluid transport was linked to Alzheimers disease. Moreover, fluid flow may be exploited to administer drugs to the brain. Using computer simulations, we estimate bulk flow velocities in the gray matter functional brain tissue due to changes in blood pressure and solute concentrations in unseen detail. We show that microvessel pulsations as filtration across the blood capillaries are potentially potent drivers of fluid flow in brain tissue.

biophysics↗

bioRxiv2022

Estimates for the astrocyte endfoot sheath permeability of the extra-cellular pathway

BackgroundAstrocyte endfoot processes are believed to cover all micro-vessels in the brain cortex and may play a significant role in fluid and substance transport into and out of the brain parenchyma. Detailed fluid mechanical models of diffusive and advective transport in the brain are promising tools to investigate theories of transport. MethodsWe derive theoretical estimates of astrocyte endfoot sheath permeability for advective and diffusive transport and its variation in microvascular networks from mouse brain cortex. The networks are based on recently published experimental data and generated endfoot patterns are based on Voronoi tessellations of the perivascular surface. We estimate corrections for projection errors in previously published data. ResultsWe provide structural-functional relationships between vessel radius and resistance that can be directly used in flow and transport simulations. We estimate endfoot sheath filtration coefficients in the range Lp = 0.2 x 10-10 m Pa-1 s-1 to 2.7 x 10-10 m Pa-1 s-1, diffusion membrane coefficients in the range CM = 0.5 x 103 m-1 to 6 x 103 m-1, and gap area fractions in the range 0.2 % to 0.6 %. ConclusionsThe astrocyte endfoot sheath surrounding microvessels forms a secondary barrier to extra-cellular transport, separating the extra-cellular space of the parenchyma and the perivascular space outside the endothelial layer. The filtration and membrane diffusion coefficients of the endfoot sheath are estimated to be an order of magnitude lower than the extra-cellular matrix while being two orders of magnitude higher than the vessel wall.

biophysics↗

bioRxiv2022

Pump-less, recirculating organ-on-a-chip (rOoC) platform

Current organ-on-a-chip (OoC) systems mimic important aspects of specific organ and tissue functions, however, many commercial and academic devices are either too simple for advanced assays or require a complicated support set-up including external driving systems such as pumps and tubing that hamper scalability and robustness. We have developed a novel, pump-less directional flow recirculating organ-on-a-chip (rOoC) platform that creates continuous or pulsed directional gravity-driven flow by a combination of a 3D-tilting system and an optimized microfluidic layout. The rOoC platform allows growing and connecting tissue or organ representations on-chip with the possibility of incorporating barrier functions, gradients, and circulating cells. Using the rOoC platform we demonstrate simple and reproducible endothelialisation, hepatic organoid integration, and the first steps of vascularization of 3D organ representations on-chip.

bioengineering↗

bioRxiv2022

Profiling Mouse Brown and White Adipocytes to Identify Metabolically Relevant Small ORFs and Functional Microproteins

The absence of thousands of recently annotated small open reading frame (smORF)-encoded peptides and small proteins (microproteins) from databases has precluded their analysis in metabolism and metabolic disease. Given the outsized importance of small proteins and peptides such as insulin, leptin, amylin, glucagon, and glucagon-like peptide-1 (GLP-1) in metabolism, microproteins are a potentially rich source of uncharacterized metabolic regulators. Here, we annotate smORFs in primary differentiated brown, white, and beige mouse adipose cells. Ribosome profiling (Ribo-Seq) detected a total of 3,877 unannotated smORFs. Analysis of RNA-Seq datasets revealed diet-regulated smORF expression in adipose tissues, and validated the adipose translation of the feeding-neuron marker gene Gm8773. Gm8773 encodes the mouse homolog of FAM237B, a neurosecretory protein that stimulates food intake and promotes weight gain in chickens. Testing of recombinant mFAM237B produced similar orexigenic activity in mice further supporting a role for FAM237B as a metabolic regulator and potentially part of the brain-adipose axis. Furthermore, we demonstrated that data independent acquisition mass spectrometry (DIA-MS) proteomics can provide a sensitive, flexible, and quantitative platform for identifying microproteins by mass spectrometry. Using this system led to the detection of 58 microproteins from cell culture and an additional 33 from mouse plasma. The proteomics data established the anti-inflammatory microprotein AW112010 as a circulating factor, and found that plasma levels of a microprotein translated from a FRS2 uORF is elevated in older obese mice. Together, the data highlight the value of this database in examining understudied smORFs and microproteins in metabolic research and identifying additional regulators of metabolism.

systems biology↗

bioRxiv2020

Autism-linked gene FoxP1 selectively regulates the cultural transmission of learned vocalizations

Autism spectrum disorders (ASD) are characterized by impaired learning of culturally transmitted behaviors like social skills, speech, and language1-3. These behaviors are learned by copying parents and other social models during development, a two-stage process that involves forming memories of appropriate behaviors during social experiences and then using those memories to guide imitation. How ASD-linked genes impair these often-intertwined aspects of learning is not known, thereby limiting our understanding of the developmental progression of ASD and the targeting of therapeutic interventions. Here we show that these aspects of learning are dissociable and that the ASD-linked gene FoxP1 selectively impairs learning from social experience, but not behavioral imitation. Haploinsufficiency of FOXP1 in humans causes FOXP1 syndrome, a neurodevelopmental disorder typified by severe disruptions in speech and language development, and other ASD-associated symptoms4,5. We tested how knockdown of FoxP1 (FP1-KD) affects the cultural transmission of vocal behaviors in zebra finches, a songbird that learns by memorizing and vocally copying the song of an adult song-tutor. We find that FP1-KD blocks song learning in juvenile birds by selectively impairing their ability to encode a memory during social experiences with a songtutor. These learning deficits are linked to disruptions in experience-driven structural and functional plasticity. However, if birds are exposed to tutor-song prior to FP1-KD, their ability to imitate that song during development is unaffected. Thus, FP1-KD impairs cultural transmission of vocalizations by disrupting the ability to form appropriate vocal memories, yet spares the ability to use previously acquired memories to guide vocal learning. This indicates that learning from social experience may be particularly vulnerable in FOXP1 syndrome.

neuroscience↗

bioRxiv2019

Call for participation: Collaborative benchmarking of functional-structural root architecture models. The case of root water uptake.

Three-dimensional models of root growth, architecture and function are becoming important tools that aid the design of agricultural management schemes and the selection of beneficial root traits. However, while benchmarking is common in many disciplines that use numerical models such as natural and engineering sciences, functional-structural root architecture models have never been systematically compared. The following reasons might induce disagreement between the simulation results of different models: different representation of root growth, sink term of root water and solute uptake and representation of the rhizosphere. Presently, the extent of discrepancies is unknown, and a framework for quantitatively comparing functional-structural root architecture models is required. We propose, in a first step, to define benchmarking scenarios that test individual components of complex models: root architecture, water flow in soil and water flow in roots. While the latter two will focus mainly on comparing numerical aspects, the root architectural models have to be compared at a conceptual level as they generally differ in process representation. Therefore defining common inputs that allow recreating reference root systems in all models will be a key challenge. In a second step, benchmarking scenarios for the coupled problems are defined. We expect that the results of step 1 will enable us to better interpret differences found in step 2. This benchmarking will result in a better understanding of the different models and contribute towards improving them. Improved models will allow us to simulate various scenarios with greater confidence and avoid bugs, numerical errors or conceptual misunderstandings. This work will set a standard for future model development.

plant biology↗

bioRxiv2018

A multi-scale sub-voxel perfusion model to estimate diffusive capillary wall conductivity in multiple sclerosis lesions from perfusion MRI data

We propose a new mathematical model to infer capillary leakage coefficients from dynamic susceptibility contrast MRI data. To this end, we derive an embedded mixed-dimension flow and transport model for brain tissue perfusion on a sub-voxel scale. This model is used to obtain the contrast agent concentration distribution in a single MRI voxel during a perfusion MRI sequence. We further present a magnetic resonance signal model for the considered sequence including a model for local susceptibility effects. This allows modeling MR signal-time curves that can be compared to clinical MRI data. The proposed model can be used as a forward model in the inverse modeling problem of inferring model parameters such as the diffusive capillary wall conductivity. Acute multiple sclerosis lesions are associated with a breach in the integrity of the blood brain barrier. Applying the model to perfusion MR data of a patient with acute multiple sclerosis lesions, we conclude that diffusive capillary wall conductivity is a good indicator for characterizing activity of lesions, even if other patient-specific model parameters are not well-known.\n\nAuthor summaryThe use of advanced brain imaging techniques has supported in-vivo research targeted to the integrity of the blood-brain barrier. We propose a new type of post-processing for raw image data using contrast agent perfusion simulations on the data-poor capillary scale. Combining modern simulation techniques with the clinical image data allows us to determine patient-specific and pathologically relevant parameters such as the capillary wall conductivity. The presented simulation model is a step towards the quantification of contrast agent leakage in the brain, which is typical for acute multiple sclerosis lesions, but also occurs with other diseases affecting the blood-brain-barrier, such as cerebral gliomas.

bioengineering↗

bioRxiv2017

Exposure to Wood Smoke is Associated with Increased Risk of Asthma and Respiratory Symptoms in a Honduran Population

BackgroundExposure to environmental pollutants has been shown to be associated with asthma, but few studies have evaluated the effect of wood smoke on asthma and disease severity in a developing country, where use of stoves powered by solid fuels is a common practice.\n\nObjectiveIn a population in Olancho, Honduras, we evaluated the association between cooking fuel, stove type and asthma. We also evaluated the effects of these factors on asthma symptoms, lung function, and atopy.\n\nMethodsParticipants with physician-diagnosed asthma (n = 597) and controls without asthma (n = 429) were recruited from the Olancho province in Honduras. Participants were interviewed using a questionnaire and their baseline pulmonary function was measured using spirometry.\n\nResultsThe prevalence of use of wood as a cooking fuel was 66.9% in the study population, of which 42.1% of participants used wood as their only fuel. Use of wood as a cooking fuel was more prevalent among households with lower income, lower maternal education, and less urbanization. The prevalence of use of an open wood stove as the primary cooking stove among participants with asthma was 6.2% higher (95% CI 0.8 - 11.7%, p = .02) than among healthy controls. In a multiple logistic regression model, we identified a significant association between use of an open wood stove and asthma (OR = 1.80, 95% CI = 1.17 - 2.78, p = 0.007), compared to the referent (electric) stove category. Among participants with asthma, we identified a significant association between use of wood as cooking fuel and increased daytime respiratory symptoms (OR = 1.46, CI: 1.01 - 2.58, p = 0.046) and nocturnal symptoms (OR = 2.51, CI: 1.04 - 2.62, p = 0.04), though not with pulmonary function. Among control participants without asthma, use of wood as cooking fuel was associated with atopy (OR = 1.94, CI = 1.14 - 3.33, p = 0.015) and cough (OR = 2.22, CI = 1.09 - 4.88, p = 0.04).\n\nConclusionsUse of an open wood stove for cooking in a developing country appears to be a significant risk factor for asthma and respiratory symptoms. Exposure to wood smoke may play a role in atopic sensitization and respiratory symptoms, leading to the development of obstructive lung disease in susceptible individuals.

epidemiology↗