Democratising deep learning for microscopy with ZeroCostDL4Mic

Deep Learning (DL) methods are powerful analytical tools for microscopy and can outperform conventional image processing pipelines. Despite the enthusiasm and innovations fuelled by DL technology, the need to access powerful and compatible resources to train DL networks leads to an accessibility barrier that novice users often find difficult to overcome. Here, we present ZeroCostDL4Mic, an entry-level platform simplifying DL access by leveraging the free, cloud-based computational resources of Google Colab. ZeroCostDL4Mic allows researchers with no coding expertise to train and apply key DL networks to perform tasks including segmentation (using U-Net and StarDist), object detection (using YOLOv2), denoising (using CARE and Noise2Void), super-resolution microscopy (using Deep-STORM), and image-to-image translation (using Label-free prediction - fnet, pix2pix and CycleGAN). Importantly, we provide suitable quantitative tools for each network to evaluate model performance, allowing model optimisation. We demonstrate the application of the platform to study multiple biological processes.

Erratum: Integrin Binding Dynamics Modulate Ligand-Specific Mechanosensing in Mammary Gland Fibroblasts

[This corrects the article DOI: 10.1016/j.isci.2020.100907.].

Integrin Binding Dynamics Modulate Ligand-Specific Mechanosensing in Mammary Gland Fibroblasts

The link between integrin activity regulation and cellular mechanosensing of tissue rigidity, especially on different extracellular matrix ligands, remains poorly understood. Here, we find that primary mouse mammary gland stromal fibroblasts (MSFs) are able to spread efficiently, generate high forces, and display nuclear YAP on soft collagen-coated substrates, resembling the soft mammary gland tissue. We describe that loss of the integrin inhibitor, SHARPIN, impedes MSF spreading specifically on soft type I collagen but not on fibronectin. Through quantitative experiments and computational modeling, we find that SHARPIN-deficient MSFs display faster force-induced unbinding of adhesions from collagen-coated beads. Faster unbinding, in turn, impairs force transmission in these cells, particularly, at the stiffness optimum observed for wild-type cells. Mechanistically, we link the impaired mechanotransduction of SHARPIN-deficient cells on collagen to reduced levels of collagen-binding integrin α11β1. Thus integrin activity regulation and α11β1 play a role in collagen-specific mechanosensing in MSFs.

Integrin signaling and mechanotransduction in regulation of somatic stem cells

Somatic stem cells are characterized by their capacity for self-renewal and differentiation, making them integral for normal tissue homeostasis. Different stem cell functions are strongly affected by the specialized microenvironment surrounding the cells. Consisting of soluble signaling factors, extracellular matrix (ECM) ligands and other cells, but also biomechanical cues such as the viscoelasticity and topography of the ECM, these factors are collectively known as the niche. Cell-ECM interactions are mediated largely by integrins, a class of heterodimeric cell adhesion molecules. Integrins bind their ligands in the extracellular space and associate with the cytoskeleton inside the cell, forming a direct mechanical link between the cells and their surroundings. Indeed, recent findings have highlighted the importance of integrins in translating biophysical cues into changes in cell signaling and function, a multistep process known as mechanotransduction. The mechanical properties of the stem cell niche are important, yet the underlying molecular details of integrin-mediated mechanotransduction in stem cells, especially the roles of the different integrin heterodimers, remain elusive. Here, we introduce the reader to the concept of integrin-mediated mechanotransduction, summarize current knowledge on the role of integrin signaling and mechanotransduction in regulation of somatic stem cell functions, and discuss open questions in the field.

[Aspects of pulmonary involvement in inflammatory bowel disease]

The incidence of pulmonary manifestations of inflammatory bowel disease (IBD) appears to be much higher than previously assumed. In prospective studies, subclinical pulmonary interstitial infiltrates or pathological lung function were found in 40%-60% of IBD patients, both in children and adults. Pulmonary disorders can affect any part of the respiratory system, the most frequent pattern being inflammation of the large airways often associated with bronchiectasis. The differential diagnosis should include drug-related pulmonary disease and infectious causes when receiving immunosuppressive therapy. The diagnostic approach consists of a thorough history and clinical status as well as lung function tests including body plethysmography and high-resolution computed tomography of the thorax. Bronchoscopy with broncheoalveolar lavage and sample collection for histology as well as exclusion of pulmonary embolism may be indicated. Pulmonary disease in association with IBD can develop at any time during the course of IBD: in rare cases, symptoms can evolve even before gastrointestinal symptoms appear. On the other hand, there are frequent reports on the occurrence of pulmonary inflammation after proctocolectomy in patients with ulcerative colitis. The pathophysiologic background is largely unknown, but there seems to be an interaction between gastrointestinal and pulmonary inflammation. The mainstay of therapy are inhaled or systemic corticosteroids. Most patterns of pulmonary involvement in IBD respond well to corticosteroid therapy. Rarely, serious and persisting complications occur, such as strictures or stenosis of the large airways.

Abstract 5067: b1-Integrin promotes inflammatory cytokine-induced vascular leakage

Increased capillary leakage is a potentially life-threatening condition associated with sepsis and cytokine release syndrome (CRS) that develops as a side effect of novel chimeric antigen receptor (CAR) T-cell cancer immunotherapies. CRS and sepsis are characterized by immune activation, resulting in elevated circulating levels of inflammatory cytokines including IL-6 and IL-1β, and thrombin that promote vascular leakage and the development of hypovolemic shock and multiorgan failure. However, molecular mechanisms behind capillary leakage remain unknown, and importantly, targeted approaches for the management of capillary leakage are limited. Here, we found that β1-integrin acts as a critical universal mediator of endothelial permeability induced by various inflammatory agents, including LPS, IL-6, IL-1β and thrombin. In a mouse model of LPS-induced systemic inflammation, resulting in increased inflammatory cytokine production and vascular leakage, function blocking antibodies against β1-integrin prevented vascular leakage and improved integrity of vascular endothelium, leading to protection from LPS-induced cardiac failure. β1-integrin blocking antibodies were effective in reducing vascular leakage even when administered after the onset of systemic inflammation and increase in the serum levels of IL-6, IL-1β and TNF-α. By using an in vitro model, we found that inflammatory agents generated mechanical stress, in a β1-integrin dependent manner, leading to endothelial cell contractility and permeability. Conclusively, our data indicates that β1-integrin promotes vascular leakage in inflammation, and that targeting this mechanism may have therapeutic utility for vascular stabilization in CRS and capillary leak syndromes associated with immune activation and systemic inflammation.

Citation Format: Elina A. Kiss, Laura Hakanpää, Guillaume Jacquemet, Ilkka Miinalainen, Martina Lerche, Camilo Guzman, Eero Mervaala, Lauri Eklund, Johanna Ivaska, Pipsa Saharinen. b1-Integrin promotes inflammatory cytokine-induced vascular leakage [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5067.

A Strong Contractile Actin Fence and Large Adhesions Direct Human Pluripotent Colony Morphology and Adhesion

Cell-type-specific functions and identity are tightly regulated by interactions between the cell cytoskeleton and the extracellular matrix (ECM). Human pluripotent stem cells (hPSCs) have ultimate differentiation capacity and exceptionally low-strength ECM contact, yet the organization and function of adhesion sites and associated actin cytoskeleton remain poorly defined. We imaged hPSCs at the cell-ECM interface with total internal reflection fluorescence microscopy and discovered that adhesions at the colony edge were exceptionally large and connected by thick ventral stress fibers. The actin fence encircling the colony was found to exert extensive Rho-ROCK-myosin-dependent mechanical stress to enforce colony morphology, compaction, and pluripotency and to define mitotic spindle orientation. Remarkably, differentiation altered adhesion organization and signaling characterized by a switch from ventral to dorsal stress fibers, reduced mechanical stress, and increased integrin activity and cell-ECM adhesion strength. Thus, pluripotency appears to be linked to unique colony organization and adhesion structure.

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Human pluripotent colonies have exceptional actin structure and focal adhesions

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Contraction-dependent tight colony compaction enforces pluripotency

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Colony morphology is maintained by edge-oriented cell divisions

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Differentiation alters actin orientation, integrin activity, and adhesion strength

AMPK negatively regulates tensin-dependent integrin activity

Georgiadou et al. show that the major metabolic sensor AMPK regulates integrin activity and integrin-dependent processes in fibroblasts by modulating tensin levels. Loss of AMPK up-regulates tensin expression, triggering enhanced integrin activity in fibrillar adhesions, fibronectin remodeling, and traction stress.

Tight regulation of integrin activity is paramount for dynamic cellular functions such as cell matrix adhesion and mechanotransduction. Integrin activation is achieved through intracellular interactions at the integrin cytoplasmic tails and through integrin–ligand binding. In this study, we identify the metabolic sensor AMP-activated protein kinase (AMPK) as a β1-integrin inhibitor in fibroblasts. Loss of AMPK promotes β1-integrin activity, the formation of centrally located active β1-integrin– and tensin-rich mature fibrillar adhesions, and cell spreading. Moreover, in the absence of AMPK, cells generate more mechanical stress and increase fibronectin fibrillogenesis. Mechanistically, we show that AMPK negatively regulates the expression of the integrin-binding proteins tensin1 and tensin3. Transient expression of tensins increases β1-integrin activity, whereas tensin silencing reduces integrin activity in fibroblasts lacking AMPK. Accordingly, tensin silencing in AMPK-depleted fibroblasts impedes enhanced cell spreading, traction stress, and fibronectin fiber formation. Collectively, we show that the loss of AMPK up-regulates tensins, which bind β1-integrins, supporting their activity and promoting fibrillar adhesion formation and integrin-dependent processes.

SHARPIN regulates collagen architecture and ductal outgrowth in the developing mouse mammary gland

SHARPIN is a widely expressed multifunctional protein implicated in cancer, inflammation, linear ubiquitination and integrin activity inhibition; however, its contribution to epithelial homeostasis remains poorly understood. Here, we examined the role of SHARPIN in mammary gland development, a process strongly regulated by epithelial-stromal interactions. Mice lacking SHARPIN expression in all cells (Sharpin^cpdm), and mice with a stromal (S100a4-Cre) deletion of Sharpin, have reduced mammary ductal outgrowth during puberty. In contrast, Sharpin^cpdm mammary epithelial cells transplanted in vivo into wild-type stroma, fully repopulate the mammary gland fat pad, undergo unperturbed ductal outgrowth and terminal differentiation. Thus, SHARPIN is required in mammary gland stroma during development. Accordingly, stroma adjacent to invading mammary ducts of Sharpin^cpdm mice displayed reduced collagen arrangement and extracellular matrix (ECM) stiffness. Moreover, Sharpin^cpdm mammary gland stromal fibroblasts demonstrated defects in collagen fibre assembly, collagen contraction and degradation in vitro Together, these data imply that SHARPIN regulates the normal invasive mammary gland branching morphogenesis in an epithelial cell extrinsic manner by controlling the organisation of the stromal ECM.

Mesoporous silica particle-PLA-PANI hybrid scaffolds for cell-directed intracellular drug delivery and tissue vascularization

Instructive materials are expected to revolutionize stem cell based tissue engineering. As many stem cell cues have adverse effects on normal tissue homeostasis, there is a need to develop bioactive scaffolds which offer locally retained and cell-targeted drug delivery for intracellular release in targeted cell populations. Further, the scaffolds need to support vascularization to promote tissue growth and function. We have developed an electrospun PLA-PANI fiber scaffold, and incorporated mesoporous silica nanoparticles within the scaffold matrix to obtain cell-targeted and localized drug delivery. The isotropy of the scaffold can be tuned to find the optimal morphology for a given application and the scaffold is electroactive to support differentiation of contractile tissues. We demonstrate that there is no premature drug release from particles under physiological conditions over a period of one week and that the drug is released upon internalization of particles by cells within the scaffold. The scaffold is biocompatible, supports muscle stem cell differentiation and cell-seeded scaffolds are vascularized in vivo upon transplantation on the chorioallantoic membrane of chicken embryos. The scaffold is a step towards instructive biomaterials for local control of stem cell differentiation, and tissue formation supported by vascularization and without adverse effects on the homeostasis of adjacent tissues due to diffusion of biological cues.

Pressure-Induced Invar Behavior in Pd3Fe

Synchrotron x-ray diffraction (XRD) measurements, nuclear forward scattering (NFS) measurements, and density functional theory (DFT) calculations were performed on L1_{2}-ordered Pd3Fe. Measurements were performed at 300 K at pressures up to 33 GPa, and at 7 GPa at temperatures up to 650 K. The NFS revealed a collapse of the 57Fe magnetic moment between 8.9 and 12.3 GPa at 300 K, coinciding with a transition in bulk modulus found by XRD. Heating the sample under a pressure of 7 GPa showed negligible thermal expansion from 300 to 523 K, demonstrating Invar behavior. Zero-temperature DFT calculations identified a ferromagnetic ground state and showed several antiferromagnetic states had comparable energies at pressures above 20 GPa.

X-ray Bragg diffraction in asymmetric backscattering geometry

We observe three effects in the Bragg diffraction of x rays in backscattering geometry from asymmetrically cut crystals. First, exact Bragg backscattering takes place not at normal incidence to the reflecting atomic planes. Second, a well-collimated (approximately 1 microrad) beam is transformed after the Bragg reflection into a strongly divergent beam (230 microrad) with reflection angle dependent on x-ray wavelength--an effect of angular dispersion. The asymmetrically cut crystal thus behaves like an optical prism, dispersing an incident collimated polychromatic beam. The dispersion rate is approximately 8.5 mrad/eV. Third, parasitic Bragg reflections accompanying Bragg backreflection are suppressed. These effects offer a radically new means for monochromatization of x rays not limited by the intrinsic width of the Bragg reflection.

Precise measurement of the lattice parameters of α-Al2O3in the temperature range 4.5–250 K using the Mössbauer wavelength standard

The lattice parameters of α-Al2O3have been measured in a temperature range from 4.5 to 250 K with a relative accuracy of better than 6 × 10−6. The experimental method uses Bragg backscattering and the recently proposed Mössbauer wavelength standard,i.e.the wavelength λM= 86.025474 (16) pm of the nuclear resonance radiation of57Fe (Shvyd'koet al., 2000), which has previously been applied successfully to measure the lattice parameters of α-Al2O3at temperatures between 286 and 374 K (Shvyd'koet al., 2002). The experimental data in the range from 4.5 to 374 K are consistent with the Debye model of thermal expansion. At 4.5 K, the thermal expansion coefficient is as low as 1.2 (9) × 10−10 K−1in theadirection.

X-ray interferometry with microelectronvolt resolution

We demonstrate an interferometer for hard x rays with two back-reflecting sapphire crystal mirrors--a prototype x-ray Fabry-Pérot interferometer. A finesse of 15 and 0.76 mu eV broad Fabry-Pérot transmission resonances are measured by the time response of the interferometer. Interference patterns are observed directly in spectral dependences of reflectivity.

Anomalous isotopic effect on the lattice parameter of silicon

The difference Delta(a)=a(30)-a(28) of the lattice parameter of 30Si and 28Si crystals is measured over a temperature range from 4.7 to 700 K. In disagreement with existing knowledge, the strongest isotopic effect is not detected at the lowest achieved temperature T=4.7 K. An anomalous behavior is observed: The relative difference |Delta(a)/a| attains its maximum value of 56.8(5) ppm at T=75(10) K. The anomalous behavior is attributed to the influence of phonon modes with negative Grüneisen parameters. At T=700 K the effect still amounts to 30% of the maximal value. The experimental data are consistent with an approach based on the density-functional perturbation theory.

gamma-Ray wavelength standard for atomic scales

The wavelength of the 57Fe Mössbauer radiation is measured with a relative uncertainty of 0.19 ppm by using almost exact Bragg backscattering from a reference silicon crystal. Its value is determined as lambda(M) = 0.860 254 74(16)x10(-10) m. The corresponding Mössbauer photon energy is E(M) = 14 412.497(3) eV. The wavelength of the 57Fe Mössbauer radiation is easily reproducible with an accuracy of at least 10(-11)lambda(M) and could be used as a length standard of atomic dimensions.

[The incidence of lung infection in patients with mucoviscidosis and the disease course with various pathogen spectra]

A retrospective review on the frequency of lung infections by the most important organisms Staphylococcus aureus and Pseudomonas aeruginosa in patients with cystic fibrosis in the GDR during the period from 1981 to 1985 revealed an average infectious rate of 58.6 per cent by Staphylococcus and of 26.9 per cent by Pseudomonas respectively. A distinct increase of the infections by Pseudomonas could only be documented from 1981 to 1982, later on the infectious rate remained nearly equal and showed only a peak value of 35.6 per cent in 1983. Thus the frequency of infections by Pseudomonas is significantly lower in the GDR than in most other countries. The comparison of the course of the disease in patients with permanent lung infection during 4 or 5 years established a mortality rate of a double amount in the group of patients with Pseudomonas colonisation versus the group with Staphylococcus colonisation. Otherwise no significant difference could be stated in the mean age of the beginning of lung infection (Staphylococcus = 9.7 years of age - Pseudomonas = 10.1 years of age). Analysing the pulmonary x-ray findings we found a significantly more rapid deterioriation during the follow-up period in patients with permanent Pseudomonas infection than in patients with permanent Staphylococcus infection, whereas the evolution of body height and weight did not take different course.