Biology subjects

Reichmann, J.

Publications and source records attributed to Reichmann, J..

6 recordsLinked to original sources

bioRxiv2025

Critical point drying of brain tissue for X-ray phase contrast imaging

X-ray phase contrast tomography is emerging as a powerful method for imaging large volumes of brain tissue at sub-cellular resolution. However, current sample preparation methods are largely inherited from visible light or electron microscopy workflows and hence are not optimised to exploit the full potential of X-ray contrast mechanisms. Here we propose to replace interstitial material by air to enhance X-ray phase contrast of the ultrastructural features. We used critical point drying (CPD) of heavy metal-stained mouse brain tissue to produce mechanically stable samples with preserved ultrastructure and enhanced refractive index boundaries, a nanofoam-like material that remains compatible with follow-up conventional resin embedding. Using two complementary synchrotron-based setups, a high-throughput microtomography beamline (P14, DESY) and a nanoscale holographic tomography beamline (ID16A, ESRF), we found that CPD samples consistently showed 2-4x stronger phase-shift signal than conventional resin-embedded tissue. The contrast gain remained consistent across samples, imaging conditions, and beamlines. Our results suggest that CPD offers a versatile route for preparing tissue for subcellular and ultrastructural-resolution X-ray imaging. It retains structural detail while improving signal, and is compatible with other processing procedures like femtosecond laser milling or electron microscopy, paving the path for biological tissue imaging beyond the mm3 scale.

neuroscience↗

bioRxiv2024

Cytoarchitecture of SARS-CoV-2 infected hamster lungs by X-ray phase contrast tomography: imaging workflow and classification for drug testing

X-ray Phase Contrast Tomography (XPCT) based on wavefield propagation has been established as a high resolution three-dimensional (3D) imaging modality, suitable to reconstruct the intricate structure of soft tissues, and the corresponding pathological alterations. However, for biomedical research, more is needed than 3D visualisation and rendering of the cytoarchitecture in a few selected cases. First, the throughput needs to be increased to cover a statistically relevant number of samples. Second, the cytoarchitecture has to be quantified in terms of morphometric parameters, independent of visual impression. Third, dimensionality reduction and classification are required for identification of effects and interpretation of results. In this work, we present a workflow implemented at a laboratory CT setup, using semi-automated data acquisition, reconstruction and statistical quantification of lung tissue in an early screen of Covid-19 drug candidates. Different drugs were tested in a hamster model after SARS-CoV-2 infection. To make full use of the recorded high-throughput XPCT data, we then used morphometric parameter determination followed by a dimensionality reduction and classification based on optimal transport. This approach allows efficient discrimination between physiological and pathological lung structure, thereby providing invaluable insights into the pathological progression and partial recovery due to drug treatment.

pathology↗

bioRxiv2023

A Myelin Map of Trunk Folds in the Elephant Trigeminal Nucleus

Elephants have elaborate trunk skills and large, but poorly understood brains. Here we study trunk representations in elephant trigeminal nuclei, which form large protrusions on the ventral brainstem. These ventral brainstem protrusions have previously been referred to as inferior olive, but a delineation of the olivo-cerebellar tract reveals these (trigeminal) nuclei are not connected to the cerebellum via climbing fibers. In contrast, the olivo-cerebellar tract connects to a large dorsolateral nucleus with a serrated cellular architecture, the putative elephant inferior olive. Dense vascularization and intense cytochrome-oxidase reactivity distinguish several elongated trigeminal putative trunk modules, which repeat in the anterior-posterior direction. We focus on the most anterior and largest of these units, the putative nucleus principalis trunk module. Module neuron density is low and non-neural cells outnumber neurons by [~]108:1. Dendritic trees are elongated along the axis of axon bundles (myelin stripes) transversing the trunk module. Synchrotron X-ray-phase-contrast tomography suggests myelin-stripe-axons transverse the trunk module. We show a remarkable correspondence of trunk module myelin stripes and trunk folds. Myelin stripes show little relation to trigeminal neurons and stripe-axons appear to often go nowhere; we suggest that myelin stripes might serve to separate trunk-fold domains rather than to connect neurons. Myelin-stripes-to-folds mapping allowed to determine neural magnification factors, which changed from 1000:1 proximally to 5:1 in the trunk finger. Asian elephants have fewer ([~]640,000) trunk-module neurons than Africans ([~]740,000) and show enlarged representations of trunk parts involved in object wrapping. The elephant trigeminal trunk module is exquisitely organized into trunk-fold-related units.

neuroscience↗

bioRxiv2017

Disruption of dual zygotic spindle assembly shows epigenetic asymmetry to be chromosome intrinsic

At the beginning of mammalian life the genetic material from each parent meets when the fertilized egg divides. It was previously thought that a single microtubule spindle is responsible to spatially combine the two genomes and then segregate them to create the two-cell embryo. Utilizing light-sheet microscopy, we showed that two bipolar spindles form in the zygote, that independently congress the maternal and paternal genomes. These two spindles aligned their poles prior to anaphase but kept the parental genomes apart during the first cleavage. This spindle assembly mechanism provides a rationale for erroneous divisions into more than two blastomeric nuclei observed in mammalian zygotes and reveals the mechanism behind the observation that parental genomes occupy separate nuclear compartments in the two-cell embryo.\n\nOne Sentence Summary: After fertilization, two spindles form around pro-nuclei in mammalian zygotes and keep the parental genomes apart during the first division.

cell biology↗

bioRxiv2017

Tex19.1 Restricts LINE-1 Mobilisation in Mouse Embryonic Stem Cells

Mobilisation of retrotransposons to new genomic locations is a significant driver of mammalian genome evolution. In humans, retrotransposon mobilisation is mediated primarily by proteins encoded by LINE-1 (L1) retrotransposons, which mobilise in pluripotent cells early in development. Here we show that TEX19.1, which is induced by developmentally programmed DNA hypomethylation, can directly interact with the L1-encoded protein L1-ORF1p, stimulate its polyubiquitylation and degradation, and restrict L1 mobilisation. We also show that TEX19.1 likely acts, at least in part, through promoting the activity of the E3 ubiquitin ligase UBR2 towards L1-ORF1p. Moreover, we show that loss of Tex19.1 increases L1-ORF1p levels and mobilisation of L1 reporters in pluripotent mouse embryonic stem cells implying that Tex19.1 prevents new retrotransposition-mediated mutations from arising in the germline genome. These data show that post-translational regulation of L1 retrotransposons plays a key role in maintaining trans-generational genome stability in the epigenetically dynamic developing mammalian germline.

genetics↗

bioRxiv2017

Tex19.1 Regulates Acetylated SMC3 Cohesin and Prevents Aneuploidy in Mouse Oocytes

Age-dependent oocyte aneuploidy, a major cause of Down syndrome, is associated with declining sister chromatid cohesion in postnatal oocytes. Here we show that cohesion in postnatal mouse oocytes is regulated by Tex19.1. We show that Tex19.1-/- oocytes have defects in the maintenance of chiasmata, mis-segregate their chromosomes during meiosis, and transmit aneuploidies to the next generation. By reconstituting aspects of this pathway in mitotic somatic cells, we show that Tex19.1 regulates an acetylated SMC3-marked subpopulation of cohesin by inhibiting the activity of the E3 ubiquitin ligase UBR2 towards specific substrates, and that UBR2 itself has a previously undescribed role in negatively regulating acetylated SMC3. Lastly, we show that acetylated SMC3 is associated with meiotic chromosome axes in oocytes, but that this is reduced in the absence of Tex19.1. These findings indicate that Tex19.1 maintains acetylated SMC3 and sister chromatid cohesion in postnatal oocytes, and prevents aneuploidy in the female germline.

genetics↗