Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data

Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated data-driven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximum-likelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, model-based hypothesis testing predicted lymphatic vessel-dependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights

Nebraska’s Natural Resource District System: Collaborative Approaches to Adaptive Groundwater Quality Governance

Nonpoint source pollution of groundwater by nitrates from agricultural activity is a persistent problem for which developing effective policy approaches has proven difficult. There is little empirical information on forms of governance or regime attributes that effectively and sustainably address agricultural nonpoint source pollution of groundwater. Nebraska’s Natural Resource District (NRD) system is a rare example of a groundwater governance regime that is putting programmes in place that are likely to generate sustainable groundwater quality outcomes. We focus on three groundwater nitrate management programmes in the state that collectively represent the broader NRD system. The research shows that four elements of Nebraska’s groundwater governance regime are fundamental to its success in addressing groundwater nitrates: 1) the local nature of governance, which builds trust among stakeholders; 2) the significant authority granted to the local districts by the state, allowing for the development of locally tailored solutions; 3) the collaborative governance approach, which allows potential scale imbalances to be overcome; and 4) the taxing authority granted to NRDs, which enables them to fund locally tailored management solutions. We find that these aspects of the NRD system have created conditions that enable adaptive, collaborative governance that positions the state well to address emerging groundwater quality challenges. We present aspects of the governance regime that are generalisable to other American states as efforts to address nitrate pollution in groundwater increase

Preparation of individual magnetic sub-levels of ⁴He(2³S₁) in a supersonic beam using laser optical pumping and magnetic hexapole focusing

We compare two different experimental techniques for the magnetic-sub-level preparation of metastable 4He in the 23S1 level in a supersonic beam, namely, magnetic hexapole focusing and optical pumping by laser radiation. At a beam velocity of v = 830 m/s, we deduce from a comparison with a particle trajectory simulation that up to 99% of the metastable atoms are in the MJ″ = +1 sub-level after magnetic hexapole focusing. Using laser optical pumping via the 23P2–23S1 transition, we achieve a maximum efficiency of 94% ± 3% for the population of the MJ″ = +1 sub-level. For the first time, we show that laser optical pumping via the 23P1–23S1 transition can be used to selectively populate each of the three MJ″ sub-levels (MJ″ = −1, 0, +1). We also find that laser optical pumping leads to higher absolute atom numbers in specific MJ″ sub-levels than magnetic hexapole focusing

Mediat. Inflamm.

There is increasing evidence that proteasomes have a biological role in the extracellular alveolar space, but inflammation could change their composition. We tested whether immunoproteasome protein-containing subpopulations are present in the alveolar space of patients with lung inflammation evoking the acute respiratory distress syndrome (ARDS). Bronchoalveolar lavage (BAL) supernatants and cell pellet lysate from ARDS patients (n = 28) and healthy subjects (n = 10) were analyzed for the presence of immunoproteasome proteins (LMP2 and LMP7) and proteasome subtypes by western blot, chromatographic purification, and 2D-dimensional gelelectrophoresis. In all ARDS patients but not in healthy subjects LMP7 and LMP2 were observed in BAL supernatants. Proteasomes purified from pooled ARDS BAL supernatant showed an altered enzyme activity ratio. Chromatography revealed a distinct pattern with 7 proteasome subtype peaks in BAL supernatant of ARDS patients that differed from healthy subjects. Total proteasome concentration in BAL supernatant was increased in ARDS (971 ng/mL perpendicular to 1116 versus 59 perpendicular to 25; P < 0.001), and all fluorogenic substrates were hydrolyzed, albeit to a lesser extent, with inhibition by epoxomicin (P = 0.0001). Thus, we identified for the first time immunoproteasome proteins and a distinct proteasomal subtype pattern in the alveolar space of ARDS patients, presumably in response to inflammation

Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage

Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells

Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells

The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space

Molecular composition of the peri-islet basement membrane in NOD mice: a barrier against destructive insulitis

Aims/hypothesisThis study examined whether the capsule which encases islets of Langerhans in the NOD mouse pancreas represents a specialised extracellular matrix (ECM) or basement membrane that protects islets from autoimmune attack.MethodsImmunofluorescence microscopy using a panel of antibodies to collagens type IV, laminins, nidogens and perlecan was performed to localise matrix components in NOD mouse pancreas before diabetes onset, at onset of diabetes and after clinical diabetes was established (2-8.5 weeks post-onset).ResultsPerlecan, a heparan sulphate proteoglycan that is characteristic of basement membranes and has not previously been investigated in islets, was localised in the peri-islet capsule and surrounding intra-islet capillaries. Other components present in the peri-islet capsule included laminin chains alpha2, beta1 and gamma1, collagen type IV alpha1 and alpha2, and nidogen 1 and 2. Collagen type IV alpha3-alpha6 were not detected. These findings confirm that the peri-islet capsule represents a specialised ECM or conventional basement membrane. The islet basement membrane was destroyed in islets where intra-islet infiltration of leucocytes marked the progression from non-destructive to destructive insulitis. No changes in basement membrane composition were observed before leucocyte infiltration.Conclusions/interpretationThese findings suggest that the islet basement membrane functions as a physical barrier to leucocyte migration into islets and that degradation of the islet basement membrane marks the onset of destructive autoimmune insulitis and diabetes development in NOD mice. The components of the islet basement membrane that we identified predict that specialised degradative enzymes are likely to function in autoimmune islet damage.H. F. Irving-Rodgers, A. F. Ziolkowski, C. R. Parish, Y. Sado, Y. Ninomiya, C. J. Simeonovic, R. J. Rodger