Isometric Immersions and the Waving of Flags

In this article we propose a novel geometric model to study the motion of a physical flag. In our approach, a flag is viewed as an isometric immersion from the square with values in R 3 satisfying certain boundary conditions at the flag pole. Under additional regularity constraints we show that the space of all such flags carries the structure of an infinite dimensional manifold and can be viewed as a submanifold of the space of all immersions. In the second part of the article we equip the space of isometric immersions with its natural kinetic energy and derive the corresponding equations of motion. This approach can be viewed in a spirit similar to Arnold's geometric picture for the motion of an incompressible fluid.

The effect of four different object properties on latency to approach in Goffin's cockatoos (Cacatua goffiniana)

Neophobia and neophilia can be lifesaving as they can facilitate foraging while avoiding predation or intoxication. We investigated the extent to which Goffin's cockatoos (Cacatua goffiniana) exhibit ecollogically relevant and quantifiable neophobic responses toward specific object properties. Twelve cockatoos were presented with 12 novel objects grouped into four distinct categories with unique features: size, color, reflective capacity, and shape. The cockatoos were tested by measuring their latency to approach a high-quality food reward for both novel and control scenarios. Age and sex did not affect the latency to approach food in the presence of a novel object in this species. Additionally, we found no significant differences between the objects of the reflective and color categories. This result is likely due to the plasticity of neophobic behavior related to the benefits and costs of approaching novel stimuli. The cockatoos were significantly slower to approach food in the presence of objects larger than their body size than objects of a similar or smaller size, a phenomenon possibly explained by the increased risk of approaching unknown objects large enough to be a potential predator. They were also significantly more hesitant to approach food in the presence of elongated objects, a phenomenon potentially explained by an ecologically relevant avoidance of snakes. The extent of this neophobia was statistically similar at a group level, indicating that avoidance of elongated and large objects could be an adaptive response aiding survival under natural circumstances and that snakes may impose strong selective pressures on this species. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

PyCoMo: a python package for community metabolic model creation and analysis

SUMMARY

PyCoMo is a python package for quick and easy generation of genome-scale compartmentalized community metabolic models that are compliant with current openCOBRA file formats. The resulting models can be used to predict (i) the maximum growth rate at a given abundance profile, (ii) the feasible community compositions at a given growth rate, and (iii) all exchange metabolites and cross-feeding interactions in a community metabolic model independent of the abundance profile; we demonstrate PyCoMo's capability by analysing methane production in a previously published simplified biogas community metabolic model.

AVAILABILITY AND IMPLEMENTATION

PyCoMo is freely available under an MIT licence at http://github.com/univieCUBE/PyCoMo, the Python Package Index, and Zenodo.

Comparative Analysis of PEG-Free and PEG-Based Self-Emulsifying Drug Delivery Systems for Enhanced Oral Bioavailability of Therapeutic (Poly) Peptides

This study aims to compare the potential of Polyethylene glycol (PEG-free and PEG-based self-emulsifying drug delivery systems (SEDDS) for the oral administration of insulin glargine (IG). Hydrophobic ion pairs (HIPs) of IG are formed using various counterions. HIPs are assessed for log P octanol/water and dissociation behavior. They are incorporated into SEDDS based on polyglycerol (PG) and zwitterionic surfactant (ZW) using response surface methodology and compared to conventional PEG-SEDDS in size, stability, and log D SEDDS/release medium . Oral IG bioavailability in PG/ZW-SEDDS and PEG-SEDDS is evaluated in rats. Among the various counterions studied, IG-BIS (bis(isotridecyl)sulfosuccinate) HIPs demonstrated the highest log P and an improved dissociation profile. PG/ZW-SEDDS and PEG-SEDDS have similar ≈40 nm sizes and are stable over 24 h. Both formulations have log D > 4 in water and >2 in 50 mM phosphate buffer pH 6.8. PG/ZW-SEDDS yielded an oral bioavailability of 2.13 ± 0.66% for IG, while the employment of PEG-SEDDS resulted in an oral bioavailability of 1.15 ± 0.35%. This study highlights the prospective utilization of PEG-free SEDDS involving the concurrent application of PG and ZW surfactants, an alternative to conventional PEG surfactants, for improved oral therapeutic (poly) peptide delivery.

Sodium-glucose cotransporter 2 inhibition in primary and secondary glomerulonephritis

BACKGROUND

The role of sodium-glucose cotransporter 2 inhibitors (SGLT2i) in the management glomerular/systemic autoimmune diseases with proteinuria in real-world clinical settings is unclear.

METHODS

This is a retrospective, observational, international cohort study. Adult patients with biopsy-proven glomerular diseases were included. The main outcome was the percentage reduction in 24-h proteinuria from SGLT2i initiation to 3, 6, 9 and 12 months. Secondary outcomes included percentage change in estimated glomerular filtration rate (eGFR), proteinuria reduction by type of disease and reduction of proteinuria ≥30% from SGLT2i initiation.

RESULTS

Four-hundred and ninety-three patients with a median age of 55 years and background therapy with renin-angiotensin system blockers were included. Proteinuria from baseline changed by -35%, -41%, -45% and -48% at 3, 6, 9 and 12 months after SGLT2i initiation, while eGFR changed by -6%, -3%, -8% and -10.5% at 3, 6, 9 and 12 months, respectively. Results were similar irrespective of the underlying disease. A correlation was found between body mass index (BMI) and percentage proteinuria reduction at last follow-up. By mixed-effects logistic regression model, serum albumin at SGLT2i initiation emerged as a predictor of ≥30% proteinuria reduction (odds ratio for albumin <3.5 g/dL, 0.53; 95% CI 0.30-0.91; P = .02). A slower eGFR decline was observed in patients achieving a ≥30% proteinuria reduction: -3.7 versus -5.3 mL/min/1.73 m2/year (P = .001). The overall tolerance to SGLT2i was good.

CONCLUSIONS

The use of SGLT2i was associated with a significant reduction of proteinuria. This percentage change is greater in patients with higher BMI. Higher serum albumin at SGLT2i onset is associated with higher probability of achieving a ≥30% proteinuria reduction.

Probing binding and occlusion of substrate in the human creatine transporter-1 by computation and mutagenesis

In chordates, energy buffering is achieved in part through phosphocreatine, which requires cellular uptake of creatine by the membrane-embedded creatine transporter (CRT1/SLC6A8). Mutations in human slc6a8 lead to creatine transporter deficiency syndrome, for which there is only limited treatment. Here, we used a combined homology modeling, molecular dynamics, and experimental approach to generate a structural model of CRT1. Our observations support the following conclusions: contrary to previous proposals, C144, a key residue in the substrate binding site, is not present in a charged state. Similarly, the side chain D458 must be present in a protonated form to maintain the structural integrity of CRT1. Finally, we identified that the interaction chain Y148-creatine-Na+ is essential to the process of occlusion, which occurs via a "hold-and-pull" mechanism. The model should be useful to study the impact of disease-associated point mutations on the folding of CRT1 and identify approaches which correct folding-deficient mutants.

Mixing Rates of the Geometrical Neutral Lorenz Model

The aim of this paper is to obtain polynomial decay of correlations of a Lorenz-like flow where the hyperbolic saddle at the origin is replaced by a neutral saddle. To do that, we take the construction of the geometrical Lorenz flow and proceed by changing the nature of the saddle fixed point at the origin by a neutral fixed point. This modification is accomplished by changing the linearised vector field in a neighbourhood of the origin for a neutral vector field. This change in the nature of the fixed point will produce polynomial tails for the Dulac times, and combined with methods of Araújo and Melbourne (used to prove exponential mixing for the classical Lorenz flow) this will ultimately lead to polynomial upper bounds of the decay of correlations for the modified flow.

Symmetrical and Mixed Tris(acyl)phosphines: Synthesis, Oxidation and Photochemistry

Herein, we present a convenient synthesis for symmetrical and mixed substituted tris(acyl)phosphines (TAPs) starting from red phosphorus. All TAPs exhibit a phosphaalkene-acylphosphine equilibrium, which was investigated in detail by variable-temperature (VT) NMR spectroscopy supported by density-functional theory (DFT) calculations. Depending on the substituents, two phosphaalkene derivatives and ten acylphosphine derivatives could be isolated. NMR spectroscopy and single-crystal X-ray crystallography enabled a clear structural assignment of these compounds. Oxidation of selected TAPs led to the formation of the corresponding tris(acyl)phosphine oxides (TAPOs). Furthermore, their spectroscopic properties as well as their photochemistry was investigated. Especially, the TAPO compounds were evaluated for their suitability as photoinitiators by CIDNP spectroscopy, photobleaching measurements and by storage stability tests.

Why are ravens smart? Exploring the social intelligence hypothesis

Ravens and other corvids are renowned for their 'intelligence'. For long, this reputation has been based primarily on anecdotes but in the last decades experimental evidence for impressive cognitive skills has accumulated within and across species. While we begin to understand the building blocks of corvid cognition, the question remains why these birds have evolved such skills. Focusing on Northern Ravens Corvus corax, I here try to tackle this question by relating current hypotheses on brain evolution to recent empirical data on challenges faced in the birds' daily life. Results show that foraging ravens meet several assumptions for applying social intelligence: (1) they meet repeatedly at foraging sites, albeit individuals have different site preferences and vary in grouping dynamics; (1) foraging groups are structured by dominance rank hierarchies and social bonds; (3) individual ravens memorize former group members and their relationship valence over years, deduce third-party relationships and use their social knowledge in daily life by supporting others in conflicts and intervening in others' affiliations. Hence, ravens' socio-cognitive skills may be strongly shaped by the 'complex' social environment experienced as non-breeders.

Analysis of inflammatory markers and tau deposits in an autopsy series of nine patients with anti-IgLON5 disease

Anti-IgLON5 disease is a rare neurological, probably autoimmune, disorder associated in many cases with a specific tauopathy. Only a few post-mortem neuropathological studies have been reported so far. Little is known about the pathogenic mechanisms that result in neurodegeneration. We investigated the neuropathology of anti-IgLON5 disease and characterized cellular and humoral inflammation. We included nine cases (six of them previously published). Median age of patients was 71 years (53-82 years), the median disease duration was 6 years (0.5-13 years), and the female to male ratio was 5:4. Six cases with a median disease duration of 9 years presented a prominent tauopathy. Five of them had a classical anti-IgLON5-related brainstem tauopathy and another presented a prominent neuronal and glial 4-repeat tauopathy, consistent with progressive supranuclear palsy (PSP). Three cases with short disease duration (median 1.25 years) only showed a primary age-related neurofibrillary pathology. Inflammatory infiltrates of T and B cells were mild to moderate and did not significantly differ between anti-IgLON5 disease cases with or without tauopathy. In contrast, we found an extensive neuropil deposition of IgG4 in the tegmentum of the brainstem, olivary nucleus, and cerebellar cortex that was most prominent in two patients with short disease duration without the typical IgLON5-related tauopathy. The IgG4 deposits were particularly prominent in the cerebellar cortex and in these regions accompanied by mild IgG1 deposits. Activated complement deposition (C9neo) was absent. Our study indicates that IgLON5-related tau pathology occurs in later disease stages and may also present a PSP-phenotype with exclusively 4-repeat neuronal and glial tau pathology. The prominent deposition of anti-IgLON5 IgG4 at predilection sites for tau pathology suggests that anti-IgLON5 antibodies precede the tau pathology. Early start of immunotherapy might prevent irreversible neuronal damage and progression of the disease, at least in a subgroup of patients.

More than urns: A multi-method pipeline for analyzing cremation burials

Burial rites of archaeological populations are frequently interpreted based on cremated remains of the human body and the urn they were deposited in. In comparison to inhumations, information about the deceased is much more limited and dependent on fragmentation, selection of body regions, taphonomic processes, and excavation techniques. So far, little attention has been paid to the context in which urns are buried. In this study, we combined archaeological techniques with anthropology, computed tomography, archaeobotany, zooarchaeology, geochemistry and isotopic approaches and conducted a detailed analysis on a case study of two Late Bronze Age urns from St. Pölten, Austria (c. 1430 and 1260 cal. BCE). The urns were recovered en-bloc and CT-scanned before the micro-excavation. Osteological and strontium isotope analysis revealed that the cremated remains comprised a young adult female and a child that died at the age of 10-12 years. Both individuals had been subject to physiological stress and were likely local. Animal bones burnt at different temperatures suggested different depositional pathways into the urn and pit as part of the pyre, food offerings, and unintentional settlement debris. Eight wild plant and five crop plant species appeared as part of the local landscape, as food offerings and fire accelerants. Sediment chemistry suggests that pyre remains were deposited around the urns during burial. Multi-element geochemistry, archaeobotany, and zooarchaeology provide insights into the Late Bronze Age environment, the process of cremation, the gathering of bones and final funerary deposition.

Price-Directed Search, Product Differentiation and Competition

Especially in many online markets, consumers can readily observe prices, but may need to inspect products further to assess their suitability. We study the effects of product differentiation and search costs on competition and market outcomes in a tractable model of price-directed consumer search. We find that: (i) firms' equilibrium pricing always induces efficient search behavior; (ii) for relatively large product differentiation, welfare distortions still occur because some consumers (may) forgo consumption; and (iii) lower search costs lead to stochastically higher prices, which increases firms' expected profits and decreases their frequency of sales. Consumer surplus often falls when search costs decrease.

An attempt to model the causal structure behind white matter aging and cognitive decline

In this diffusion tension imaging study, voxel wise structural equation modeling was used to unravel the relation between white matter, cognition, and age. Four neurocognitive ageing models describing the interplay between age, white matter integrity, and cognition were investigated but only two models survived an Akaike information criterion-based model selection procedure. The independent factor model predicts that there is no relation between white matter integrity and cognition although both systems are affected by age. The cognitive mediation model predicts that the relation between age and white matter integrity is mediated through cognition. Roughly 60% of the observed voxels were in agreement with the independent factor model while 16% of the observed voxels were in agreement with the cognitive mediation model. Imaging results of the latter model suggest that the deterioration of fibers-that connect the two hemispheres with each other-is partly caused by an age-related decline in cognitive functioning.

Are you better than me? Social comparisons in carrion crows (Corvus corone)

Comparing oneself to others is a key process in humans that allows individuals to gauge their performances and abilities and thus develop and calibrate their self-image. Little is known about its evolutionary foundations. A key feature of social comparison is the sensitivity to other individuals' performance. Recent studies on primates produced equivocal results, leading us to distinguish between a 'strong' variant of the social comparison hypothesis formulated for humans and a 'weak' variant found in non-human primates that would comprise some elements of human social comparison. Here, we focus on corvids that are distantly related to primates and renowned for their socio-cognitive skills. We were interested in whether crows' task performances were influenced (i) by the presence of a conspecific co-actor performing the same discrimination task and (ii) by the simulated acoustic cues of a putative co-actor performing better or worse than themselves. Crows reached a learning criterion quicker when tested simultaneously as compared to when tested alone, indicating a facilitating effect of social context. The performance of a putative co-actor influenced their performance: crows were better at discriminating familiar images when their co-actor was better than they were. Standard extremity (how pronounced the difference was between the performance of the subject and that of the co-actor), and category membership (affiliation status and sex), of the putative co-actors had no effect on their performance. Our findings are in line with the 'weak' variant of social comparison and indicate that elements of human social comparison can be found outside of primates.

The reinforcement sensitivity theory affects questionnaire (RST-AQ). A validation study of a new scale targeting affects related to anxiety, approach motivation and fear

This paper presents the RST-AQ, a 22-item scale to measure the affective states related to the three motivational systems postulated by Reinforcement Sensitivity theory (RST-AQ): the Behavioral approach system (BAS), Behavioral inhibition system (BIS), and the Fight-Flight-Freeze system (FFFS). The three subscales are internally consistent. Results show an overall support for construct validity of our RST-AQ measure. The correlations of the RST-AQ subscales with other measures demonstrate a good convergent and divergent validity with regard to the subscales of BAS and BIS. The RTS-AQ Scale provides researcher with the first instrument to measures the affective states of the RST theory.

Towards liver segmentation in the wild via contrastive distillation

PURPOSE

Automatic liver segmentation is a key component for performing computer-assisted hepatic procedures. The task is challenging due to the high variability in organ appearance, numerous imaging modalities, and limited availability of labels. Moreover, strong generalization performance is required in real-world scenarios. However, existing supervised methods cannot be applied to data not seen during training (i.e. in the wild) because they generalize poorly.

METHODS

We propose to distill knowledge from a powerful model with our novel contrastive distillation scheme. We use a pre-trained large neural network to train our smaller model. A key novelty is to map neighboring slices close together in the latent representation, while mapping distant slices far away. Then, we use ground-truth labels to learn a U-Net style upsampling path and recover the segmentation map.

RESULTS

The pipeline is proven to be robust enough to perform state-of-the-art inference on target unseen domains. We carried out an extensive experimental validation using six common abdominal datasets, covering multiple modalities, as well as 18 patient datasets from the Innsbruck University Hospital. A sub-second inference time and a data-efficient training pipeline make it possible to scale our method to real-world conditions.

CONCLUSION

We propose a novel contrastive distillation scheme for automatic liver segmentation. A limited set of assumptions and superior performance to state-of-the-art techniques make our method a candidate for application to real-world scenarios.

The rete mirabile: a possible control site for swimbladder function

In a recent study, a large number of transport proteins was detected in the transcriptome and proteome of saline perfused rete mirabile tissue of the European eel. In this study, the data set was reanalyzed for the presence of receptor proteins and proteins involved in intracellular signaling pathways. A large number of expressed receptor proteins and proteins involved in intracellular signal transduction was detected. Several G-protein-coupled receptor signal pathways were significantly enriched in their expression level, in particular receptors and signaling pathways involved in the control of blood flow. The enriched signaling pathways also include pathways involved in trafficking of crucial transport proteins like, monocarboxylate transporters, V-ATPase, and aquaporin. The data, therefore, suggest that the rete mirabile has the capacity to control swimbladder function by regulating blood flow and by modifying countercurrent multiplication.

[Videoconference Fatigue Coping Strategies]

The COVID-19 pandemic has changed people's professional and private lives globally and has led to an increasing use of digital technologies, especially video conferencing systems (e.g. Zoom, Webex, Teams, Skype). Despite the possible advantages of these systems (e.g. savings in emissions by avoiding travelling), a negative phenomenon has been reported in science and practice: Videoconference Fatigue (VCF) (often synonymously referred to as Zoom Fatigue). This term describes the exhaustion and fatigue that results from the use of videoconferencing systems. In this article we report on an analysis of the academic literature, the aim of which is to document the current state of research on coping strategies. The analysis of coping strategies helps to better understand the phenomenon of VCF and to prevent or reduce fatigue and exhaustion. Furthermore, the results reported here are a basis for future work. Specifically, as of May 2022, we have identified 48 scientific articles on VCF, 37 of which also deal with coping strategies. We divide these strategies into organizational (e.g. taking breaks during and between meetings), personal (e.g. avoiding multitasking) and technological (e.g. use of the "together mode" in Teams). An important finding of our analysis is that with the exception of one paper, the effectiveness of the coping strategies has not yet been empirically examined and thus proven. This opens up enormous future research potential.

Tyrosine phosphorylation of YAP-1 in biliary epithelial cells mediates posthepatectomy liver regeneration and is affected by serotonin

Experimental data suggested activation of yes-associated protein (YAP-1) as a critical regulator of liver regeneration (LR). Serotonin (5-HT) promotes LR in rodent models and has been proposed to act via YAP-1. How 5-HT affects LR is incompletely understood. A possible mechanism how 5-HT affects human LR was explored. Sixty-one patients were included. Tissue samples prior and 2 h after induction of LR were collected. Circulating levels of 5-HT and osteopontin (OPN) were assessed. YAP-1, its phosphorylation states, cytokeratin 19 (CK-19) and OPN were assessed using immunofluorescence. A mouse model of biliary epithelial cells (BECs) specific deletion of YAP/TAZ was developed. YAP-1 increased as early as 2 h after induction of LR (p = 0.025) predominantly in BECs. BEC specific deletion of YAP/TAZ reduced LR after 70% partial hepatectomy in mice (Ki67%, p < 0.001). SSRI treatment, depleting intra-platelet 5-HT, abolished YAP-1 and OPN induction upon LR. Portal vein 5-HT levels correlated with intrahepatic YAP-1 expression upon LR (R = 0.703, p = 0.035). OPN colocalized with YAP-1 in BECs and its circulating levels increased in the liver vein 2 h after induction of LR (p = 0.017). In the context of LR tyrosine-phosphorylated YAP-1 significantly increased (p = 0.042). Stimulating BECs with 5-HT resulted in increased YAP-1 activation via tyrosine-phosphorylation and subsequently increased OPN expression. BECs YAP-1 appears to be critical for LR in mice and humans. Our evidence suggests that 5-HT, at least in part, exerts its pro-regenerative effects via YAP-1 tyrosine-phosphorylation in BECs and subsequent OPN-dependent paracrine immunomodulation.

An interdisciplinary approach to Iron Age Mediterranean chronology through combined archaeological and 14C-radiometric evidence from Sidon, Lebanon

The construction of the Iron Age Mediterranean chronology began in the Levant based on historical evidence and has been additionally supported in recent decades by means of radiocarbon analysis, although with variable precision and ratification. It is only in recent years that new evidence in the Aegean and the western Mediterranean has opened discussion towards its further acceptance as an authoritative i.e. highly reliable, and widely applicable historiographic network. Altogether, the Mediterranean Iron Age chronology has only undergone minor changes during the last hundred years. The Phoenician metropolis of Sidon in southern Lebanon now provides a new, large and robust dataset obtained through a combination of archaeological and 14C-radiometric analysis of materials from stratified contexts that allow their statistical assessment. The appearance of substantial amounts of pottery of Greek, Cypriot and Egyptian origin together with Phoenician local wares in a long stratigraphy is a benefit for the synchronisation of regional pottery styles and allows wider geographic correlation of relative chronological systems. The close association of the archaeological data with a long series of AMS-14C-dates on short-lived samples provides new evidence for the absolute dating of many of the regional pottery styles that are represented in the stratigraphy of Sidon, and contributes towards a considerable improvement of the Mediterranean chronology.

The NOGO receptor NgR2, a novel αVβ3 integrin effector, induces neuroendocrine differentiation in prostate cancer

Androgen deprivation therapies aimed to target prostate cancer (PrCa) are only partially successful given the occurrence of neuroendocrine PrCa (NEPrCa), a highly aggressive and highly metastatic form of PrCa, for which there is no effective therapeutic approach. Our group has demonstrated that while absent in prostate adenocarcinoma, the αVβ3 integrin expression is increased during PrCa progression toward NEPrCa. Here, we show a novel pathway activated by αVβ3 that promotes NE differentiation (NED). This novel pathway requires the expression of a GPI-linked surface molecule, NgR2, also known as Nogo-66 receptor homolog 1. We show here that NgR2 is upregulated by αVβ3, to which it associates; we also show that it promotes NED and anchorage-independent growth, as well as a motile phenotype of PrCa cells. Given our observations that high levels of αVβ3 and, as shown here, of NgR2 are detected in human and mouse NEPrCa, our findings appear to be highly relevant to this aggressive and metastatic subtype of PrCa. This study is novel because NgR2 role has only minimally been investigated in cancer and has instead predominantly been analyzed in neurons. These data thus pave new avenues toward a comprehensive mechanistic understanding of integrin-directed signaling during PrCa progression toward a NE phenotype.

Superhuman performance on sepsis MIMIC-III data by distributional reinforcement learning

We present a novel setup for treating sepsis using distributional reinforcement learning (RL). Sepsis is a life-threatening medical emergency. Its treatment is considered to be a challenging high-stakes decision-making problem, which has to procedurally account for risk. Treating sepsis by machine learning algorithms is difficult due to a couple of reasons: There is limited and error-afflicted initial data in a highly complex biological system combined with the need to make robust, transparent and safe decisions. We demonstrate a suitable method that combines data imputation by a kNN model using a custom distance with state representation by discretization using clustering, and that enables superhuman decision-making using speedy Q-learning in the framework of distributional RL. Compared to clinicians, the recovery rate is increased by more than 3% on the test data set. Our results illustrate how risk-aware RL agents can play a decisive role in critical situations such as the treatment of sepsis patients, a situation acerbated due to the COVID-19 pandemic (Martineau 2020). In addition, we emphasize the tractability of the methodology and the learning behavior while addressing some criticisms of the previous work (Komorowski et al. 2018) on this topic.

The cation exchanger Letm1, circadian rhythms, and NAD(H) levels interconnect in diurnal zebrafish

Mitochondria are fundamental for life and require balanced ion exchange to maintain proper functioning. The mitochondrial cation exchanger LETM1 sparks interest because of its pathophysiological role in seizures in the Wolf Hirschhorn Syndrome (WHS). Despite observation of sleep disorganization in epileptic WHS patients, and growing studies linking mitochondria and epilepsy to circadian rhythms, LETM1 has not been studied from the chronobiological perspective. Here we established a viable letm1 knock-out, using the diurnal vertebrate Danio rerio to study the metabolic and chronobiological consequences of letm1 deficiency. We report diurnal rhythms of Letm1 protein levels in wild-type fish. We show that mitochondrial nucleotide metabolism is deregulated in letm1-/- mutant fish, the rate-limiting enzyme of NAD+ production is up-regulated, while NAD+ and NADH pools are reduced. These changes were associated with increased expression amplitude of circadian core clock genes in letm1-/- compared with wild-type under light/dark conditions, suggesting decreased NAD(H) levels as a possible mechanism for circadian system perturbation in Letm1 deficiency. Replenishing NAD pool may ameliorate WHS-associated sleep and neurological disorders.

Surface chemistry on a polarizable surface: Coupling of CO with KTaO3(001)

Polarizable materials attract attention in catalysis because they have a free parameter for tuning chemical reactivity. Their surfaces entangle the dielectric polarization with surface polarity, excess charge, and orbital hybridization. How this affects individual adsorbed molecules is shown for the incipient ferroelectric perovskite KTaO₃. This intrinsically polar material cleaves along (001) into KO- and TaO₂-terminated surface domains. At TaO₂ terraces, the polarity-compensating excess electrons form a two-dimensional electron gas and can also localize by coupling to ferroelectric distortions. TaO₂ terraces host two distinct types of CO molecules, adsorbed at equivalent lattice sites but charged differently as seen in atomic force microscopy/scanning tunneling microscopy. Temperature-programmed desorption shows substantially stronger binding of the charged CO; in density functional theory calculations, the excess charge favors a bipolaronic configuration coupled to the CO. These results pinpoint how adsorption states couple to ferroelectric polarization.

Toward protein NMR at physiological concentrations by hyperpolarized water-Finding and mapping uncharted conformational spaces

Nuclear magnetic resonance (NMR) spectroscopy is a key method for determining the structural dynamics of proteins in their native solution state. However, the low sensitivity of NMR typically necessitates nonphysiologically high sample concentrations, which often limit the relevance of the recorded data. We show how to use hyperpolarized water by dissolution dynamic nuclear polarization (DDNP) to acquire protein spectra at concentrations of 1 μM within seconds and with a high signal-to-noise ratio. The importance of approaching physiological concentrations is demonstrated for the vital MYC-associated factor X, which we show to switch conformations when diluted. While in vitro conditions lead to a population of the well-documented dimer, concentrations lowered by more than two orders of magnitude entail dimer dissociation and formation of a globularly folded monomer. We identified this structure by integrating DDNP with computational techniques to overcome the often-encountered constraint of DDNP of limited structural information provided by the typically detected one-dimensional spectra.

Rewiring of Gene Expression in Pseudomonas aeruginosa During Diauxic Growth Reveals an Indirect Regulation of the MexGHI-OpmD Efflux Pump by Hfq

In Pseudomonas aeruginosa, the RNA chaperone Hfq and the catabolite repression protein Crc act in concert to regulate numerous genes during carbon catabolite repression (CCR). After alleviation of CCR, the RNA CrcZ sequesters Hfq/Crc, which leads to a rewiring of gene expression to ensure the consumption of less preferred carbon and nitrogen sources. Here, we performed a multiomics approach by assessing the transcriptome, translatome, and proteome in parallel in P. aeruginosa strain O1 during and after relief of CCR. As Hfq function is impeded by the RNA CrcZ upon relief of CCR, and Hfq is known to impact antibiotic susceptibility in P. aeruginosa, emphasis was laid on links between CCR and antibiotic susceptibility. To this end, we show that the mexGHI-opmD operon encoding an efflux pump for the antibiotic norfloxacin and the virulence factor 5-Methyl-phenazine is upregulated after alleviation of CCR, resulting in a decreased susceptibility to the antibiotic norfloxacin. A model for indirect regulation of the mexGHI-opmD operon by Hfq is presented.

Early human trophoblast development: from morphology to function

Human pregnancy depends on the proper development of the embryo prior to implantation and the implantation of the embryo into the uterine wall. During the pre-implantation phase, formation of the morula is followed by internalization of blastomeres that differentiate into the pluripotent inner cell mass lineage, while the cells on the surface undergo polarization and differentiate into the trophectoderm of the blastocyst. The trophectoderm mediates apposition and adhesion of the blastocyst to the uterine epithelium. These processes lead to a stable contact between embryonic and maternal tissues, resulting in the formation of a new organ, the placenta. During implantation, the trophectoderm cells start to differentiate and form the basis for multiple specialized trophoblast subpopulations, all of which fulfilling specific key functions in placentation. They either differentiate into polar cells serving typical epithelial functions, or into apolar invasive cells that adapt the uterine wall to progressing pregnancy. The composition of these trophoblast subpopulations is crucial for human placenta development and alterations are suggested to result in placenta-associated pregnancy pathologies. This review article focuses on what is known about very early processes in human reproduction and emphasizes on morphological and functional aspects of early trophoblast differentiation and subpopulations.

Overexpression of recombinant proteins containing non-canonical amino acids in Vibrio natriegens: p-azido-L-phenylalanine as coupling site for 19F-tags

Vibrio natriegens is the fastest growing organism identified so far. The minimum doubling time of only 9.4 min, the ability to utilize over 60 different carbon sources and its non-pathogenic properties make it an interesting alternative to E. coli as a new production host for recombinant proteins. We investigated the ability of the engineered V. natriegens strain, Vmax™ Express, to incorporate the non-canonical amino acid (ncAA) p-azido-L-phenylalanine (AzF) into recombinant proteins for NMR applications. AzF was incorporated into enhanced yellow fluorescent protein (EYFP) and MlaC, an intermembrane transport protein, by stop codon suppression. AzF incorporation into EYFP resulted in an improved suppression efficiency (SE) of up to 35.5 ± 0.8% and a protein titer of 26.7 ± 0.7 mg/L. The expression levels of MlaC-AzF even exceeded those of E. coli BL21 cells. For the recording of ¹H-¹⁵N and ¹⁹F NMR spectra, EYFP-AzF was expressed and isotopically labeled in minimal medium and the newly introduced azido-group was used as coupling site for NMR sensitive ¹⁹F-tags. Our findings show that Vmax is a flexible expression host, suitable for the incorporation of ncAAs in recombinant proteins with the potential to surpass protein yields of E. coli. The presented method suggests the implementation of V. natriegens for expression of isotopically labeled proteins containing ncAAs, which can be chemically modified for the application in protein-observed ¹⁹F-NMR.

Fos regulates macrophage infiltration against surrounding tissue resistance by a cortical actin-based mechanism in Drosophila

The infiltration of immune cells into tissues underlies the establishment of tissue-resident macrophages and responses to infections and tumors. Yet the mechanisms immune cells utilize to negotiate tissue barriers in living organisms are not well understood, and a role for cortical actin has not been examined. Here, we find that the tissue invasion of Drosophila macrophages, also known as plasmatocytes or hemocytes, utilizes enhanced cortical F-actin levels stimulated by the Drosophila member of the fos proto oncogene transcription factor family (Dfos, Kayak). RNA sequencing analysis and live imaging show that Dfos enhances F-actin levels around the entire macrophage surface by increasing mRNA levels of the membrane spanning molecular scaffold tetraspanin TM4SF, and the actin cross-linking filamin Cheerio, which are themselves required for invasion. Both the filamin and the tetraspanin enhance the cortical activity of Rho1 and the formin Diaphanous and thus the assembly of cortical actin, which is a critical function since expressing a dominant active form of Diaphanous can rescue the Dfos macrophage invasion defect. In vivo imaging shows that Dfos enhances the efficiency of the initial phases of macrophage tissue entry. Genetic evidence argues that this Dfos-induced program in macrophages counteracts the constraint produced by the tension of surrounding tissues and buffers the properties of the macrophage nucleus from affecting tissue entry. We thus identify strengthening the cortical actin cytoskeleton through Dfos as a key process allowing efficient forward movement of an immune cell into surrounding tissues.

The infiltration of immune cells into tissue underlies the establishment of tissue-resident macrophages, and responses to infections and tumors, but how do they overcome tissue barriers? This study shows that macrophages upregulate the proto-oncogene Fos, increasing the density and crosslinking of cortical actin, thereby counteracting the tension of surrounding tissues and protecting the macrophage nucleus.

Expression of transport proteins in the rete mirabile of european silver and yellow eel

BACKGROUND

In physoclist fishes filling of the swimbladder requires acid secretion of gas gland cells to switch on the Root effect and subsequent countercurrent concentration of the initial gas partial pressure increase by back-diffusion of gas molecules in the rete mirabile. It is generally assumed that the rete mirabile functions as a passive exchanger, but a detailed analysis of lactate and water movements in the rete mirabile of the eel revealed that lactate is diffusing back in the rete. In the present study we therefore test the hypothesis that expression of transport proteins in rete capillaries allows for back-diffusion of ions and metabolites, which would support the countercurrent concentrating capacity of the rete mirabile. It is also assumed that in silver eels, the migratory stage of the eel, the expression of transport proteins would be enhanced.

RESULTS

Analysis of the transcriptome and of the proteome of rete mirabile tissue of the European eel revealed the expression of a large number of membrane ion and metabolite transport proteins, including monocarboxylate and glucose transport proteins. In addition, ion channel proteins, Ca2+-ATPase, Na+/K+-ATPase and also F1F0-ATP synthase were detected. In contrast to our expectation in silver eels the expression of these transport proteins was not elevated as compared to yellow eels. A remarkable number of enzymes degrading reactive oxygen species (ROS) was detected in rete capillaries.

CONCLUSIONS

Our results reveal the expression of a large number of transport proteins in rete capillaries, so that the back diffusion of ions and metabolites, in particular lactate, may significantly enhance the countercurrent concentrating ability of the rete. Metabolic pathways allowing for aerobic generation of ATP supporting secondary active transport mechanisms are established. Rete tissue appears to be equipped with a high ROS defense capacity, preventing damage of the tissue due to the high oxygen partial pressures generated in the countercurrent system.

Ecophysiological, morphological, and biochemical traits of free-living Diplosphaera chodatii (Trebouxiophyceae) reveal adaptation to harsh environmental conditions

Single-celled green algae within the Trebouxiophyceae (Chlorophyta) are typical components of terrestrial habitats, which often exhibit harsh environmental conditions for these microorganisms. This study provides a detailed overview of the ecophysiological, biochemical, and ultrastructural traits of an alga living on tree bark. The alga was isolated from a cypress tree in the Botanical Garden of Innsbruck (Austria) and identified by morphology and molecular phylogeny as Diplosphaera chodatii. Transmission electron microscopy after high-pressure freezing (HPF) showed an excellent preservation of the ultrastructure. The cell wall was bilayered with a smooth inner layer and an outer layer of polysaccharides with a fuzzy hair-like appearance that could possibly act as cell-cell adhesion mechanism and hence as a structural precursor supporting biofilm formation together with the mucilage observed occasionally. The photosynthetic-irradiance curves of D. chodatii indicated low light requirements without photoinhibition at high photon flux densities (1580 μmol photons m^-2 s^-1) supported by growth rate measurements. D. chodatii showed a high desiccation tolerance, as 85% of its initial value was recovered after controlled desiccation at a relative humidity of ~10%. The alga contained the low molecular weight carbohydrates sucrose and sorbitol, which probably act as protective compounds against desiccation. In addition, a new but chemically not elucidated mycosporine-like amino acid was detected with a molecular mass of 332 g mol^-1 and an absorption maximum of 324 nm. The presented data provide various traits which contribute to a better understanding of the adaptive mechanisms of D. chodatii to terrestrial habitats.

Disease control as an optimization problem

In the context of epidemiology, policies for disease control are often devised through a mixture of intuition and brute-force, whereby the set of logically conceivable policies is narrowed down to a small family described by a few parameters, following which linearization or grid search is used to identify the optimal policy within the set. This scheme runs the risk of leaving out more complex (and perhaps counter-intuitive) policies for disease control that could tackle the disease more efficiently. In this article, we use techniques from convex optimization theory and machine learning to conduct optimizations over disease policies described by hundreds of parameters. In contrast to past approaches for policy optimization based on control theory, our framework can deal with arbitrary uncertainties on the initial conditions and model parameters controlling the spread of the disease, and stochastic models. In addition, our methods allow for optimization over policies which remain constant over weekly periods, specified by either continuous or discrete (e.g.: lockdown on/off) government measures. We illustrate our approach by minimizing the total time required to eradicate COVID-19 within the Susceptible-Exposed-Infected-Recovered (SEIR) model proposed by Kissler et al. (March, 2020).

Individual Goffin´s cockatoos (Cacatua goffiniana) show flexible targeted helping in a tool transfer task

Flexible targeted helping is considered an advanced form of prosocial behavior in hominoids, as it requires the actor to assess different situations that a conspecific may be in, and to subsequently flexibly satisfy different needs of that partner depending on the nature of those situations. So far, apart from humans such behaviour has only been experimentally shown in chimpanzees and in Eurasian jays. Recent studies highlight the prosocial tendencies of several bird species, yet flexible targeted helping remained untested, largely due to methodological issues as such tasks are generally designed around tool-use, and very few bird species are capable of tool-use. Here, we tested Goffin's cockatoos, which proved to be skilled tool innovators in captivity, in a tool transfer task in which an actor had access to four different objects/tools and a partner to one of two different apparatuses that each required one of these tools to retrieve a reward. As expected from this species, we recorded playful object transfers across all conditions. Yet, importantly and similar to apes, three out of eight birds transferred the correct tool more often in the test condition than in a condition that also featured an apparatus but no partner. Furthermore, one of these birds transferred that correct tool first more often before transferring any other object in the test condition than in the no-partner condition, while the other two cockatoos were marginally non-significantly more likely to do so. Additionally, there was no difference in the likelihood of the correct tool being transferred first for either of the two apparatuses, suggesting that these birds flexibly adjusted what to transfer based on their partner´s need. Future studies should focus on explanations for the intra-specific variation of this behaviour, and should test other parrots and other large-brained birds to see how this can be generalized across the class and to investigate the evolutionary history of this trait.

Outer membrane vesicles as versatile tools for therapeutic approaches

Budding of the bacterial surface results in the formation and secretion of outer membrane vesicles, which is a conserved phenomenon observed in Gram-negative bacteria. Recent studies highlight that these sphere-shaped facsimiles of the donor bacterium's surface with enclosed periplasmic content may serve multiple purposes for their host bacterium. These include inter- and intraspecies cell-cell communication, effector delivery to target cells and bacterial adaptation strategies. This review provides a concise overview of potential medical applications to exploit outer membrane vesicles for therapeutic approaches. Due to the fact that outer membrane vesicles resemble the surface of their donor cells, they represent interesting nonliving candidates for vaccine development. Furthermore, bacterial donor species can be genetically engineered to display various proteins and glycans of interest on the outer membrane vesicle surface or in their lumen. Outer membrane vesicles also possess valuable bioreactor features as they have the natural capacity to protect, stabilize and enhance the activity of luminal enzymes. Along these features, outer membrane vesicles not only might be suitable for biotechnological applications but may also enable cell-specific delivery of designed therapeutics as they are efficiently internalized by nonprofessional phagocytes. Finally, outer membrane vesicles are potent modulators of our immune system with pro- and anti-inflammatory properties. A deeper understanding of immunoregulatory effects provoked by different outer membrane vesicles is the basis for their possible future applications ranging from inflammation and immune response modulation to anticancer therapy.

Crosstalk between H2A variant-specific modifications impacts vital cell functions

Selection of C-terminal motifs participated in evolution of distinct histone H2A variants. Hybrid types of variants combining motifs from distinct H2A classes are extremely rare. This suggests that the proximity between the motif cases interferes with their function. We studied this question in flowering plants that evolved sporadically a hybrid H2A variant combining the SQ motif of H2A.X that participates in the DNA damage response with the KSPK motif of H2A.W that stabilizes heterochromatin. Our inventory of PTMs of H2A.W variants showed that in vivo the cell cycle-dependent kinase CDKA phosphorylates the KSPK motif of H2A.W but only in absence of an SQ motif. Phosphomimicry of KSPK prevented DNA damage response by the SQ motif of the hybrid H2A.W/X variant. In a synthetic yeast expressing the hybrid H2A.W/X variant, phosphorylation of KSPK prevented binding of the BRCT-domain protein Mdb1 to phosphorylated SQ and impaired response to DNA damage. Our findings illustrate that PTMs mediate interference between the function of H2A variant specific C-terminal motifs. Such interference could explain the mutual exclusion of motifs that led to evolution of H2A variants.

Quantum Polar Duality and the Symplectic Camel: A New Geometric Approach to Quantization

We define and study the notion of quantum polarity, which is a kind of geometric Fourier transform between sets of positions and sets of momenta. Extending previous work of ours, we show that the orthogonal projections of the covariance ellipsoid of a quantum state on the configuration and momentum spaces form what we call a dual quantum pair. We thereafter show that quantum polarity allows solving the Pauli reconstruction problem for Gaussian wavefunctions. The notion of quantum polarity exhibits a strong interplay between the uncertainty principle and symplectic and convex geometry and our approach could therefore pave the way for a geometric and topological version of quantum indeterminacy. We relate our results to the Blaschke-Santaló inequality and to the Mahler conjecture. We also discuss the Hardy uncertainty principle and the less-known Donoho-Stark principle from the point of view of quantum polarity.

Preserved intention understanding during moral judgments in schizophrenia

INTRODUCTION

Although there is convincing evidence for socio-cognitive impairments in schizophrenia spectrum disorder (SSD), little evidence is found for deficient moral cognition. We investigated whether patients with SSD showed altered moral judgments in a story task where the protagonist either had a neutral or malicious intention towards another person. This paradigm examined whether SSD relates to altered moral cognition in general or specifically to impaired integration of prior information (such as beliefs) in moral judgments.

METHODS

23 patients and 32 healthy controls read vignettes created in a 2 x 2 design. The protagonist in each story either had a neutral or negative intention towards another person which, as a result, either died (negative outcome) or did not die (neutral outcome). Participants rated the moral permissibility of the protagonist's action. Standard null hypothesis significance testing and equivalent Bayes analyses are reported.

RESULTS

Schizophrenia patients did not differ significantly in permissibility ratings from healthy controls. This finding was supported by the Bayes analyses which favoured the null hypothesis. Task performance was not related to symptom severity or medication.

CONCLUSIONS

The current findings do not support the notion that moral judgments are deficient in schizophrenia. Furthermore, the current study shows that patients do not have observable difficulties in integrating the protagonist's belief in the rating of the moral permissibility of the action-outcome.

Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport

The interior of a eukaryotic cell is a highly complex composite material which consists of water, structural scaffoldings, organelles, and various biomolecular solutes. All these components serve as obstacles that impede the motion of vesicles. Hence, it is hypothesized that any alteration of the cytoskeletal network may directly impact or even disrupt the vesicle transport. A disruption of the vesicle-mediated cell transport is thought to contribute to several severe diseases and disorders, such as diabetes, Parkinson’s and Alzheimer’s disease, emphasizing the clinical relevance. To address the outlined objective, a multiscale finite element model of the diffusive vesicle transport is proposed on the basis of the concept of homogenization, owed to the complexity of the cytoskeletal network. In order to study the microscopic effects of specific nanoscopic actin filament network alterations onto the vesicle transport, a parametrized three-dimensional geometrical model of the actin filament network was generated on the basis of experimentally observed filament densities and network geometries in an adenocarcinomic human alveolar basal epithelial cell. Numerical analyzes of the obtained effective diffusion properties within two-dimensional sampling domains of the whole cell model revealed that the computed homogenized diffusion coefficients can be predicted statistically accurate by a simple two-parameter power law as soon as the inaccessible area fraction, due to the obstacle geometries and the finite size of the vesicles, is known. This relationship, in turn, leads to a massive reduction in computation time and allows to study the impact of a variety of different cytoskeletal alterations onto the vesicle transport. Hence, the numerical simulations predicted a 35% increase in transport time due to a uniformly distributed four-fold increase of the total filament amount. On the other hand, a hypothetically reduced expression of filament cross-linking proteins led to sparser filament networks and, thus, a speed up of the vesicle transport.

Many vital processes in our eukaryotic cells and organs require an astonishingly precise routing of intermediate products to various intra- and extracellular destinations using vesicles as transporters. This can be illustrated by numerous examples, such as the production and destruction of proteins, the export of neurotransmitters or insulin to the extracellular domain, etc. However, the inside of a cell is tightly packed with numerous structural scaffoldings (filaments), which serve as obstacles and impede the vesicle motion. It is thought that any disturbances of the vesicle-mediated cell transport contribute to numerous degenerative diseases and disorders, which highlights the clinical relevance for investigating this intracellular transport mechanism by developing computational models and performing experimental studies. In this study, we numerically quantified how different specific alterations of the filament density inside a human lung cell—due to changed mechanical loadings or genetic disorders of proteins being responsible for filament branching—affect the diffusion of vesicles inside the intracellular fluid. Therefore, based on the concept of homogenization, a computationally efficient numerical method was developed and utilized to simulate the diffusion of vesicles inside the whole cell, considering the detailed structural information of the filament network.

Demand-side or supply-side stabilisation policies in a small euro area economy: a case study for Slovenia

In this paper we analyse the effectiveness of demand- and supply-side fiscal policies in the small open economy of Slovenia. Simulating the SLOPOL10 model, an econometric model of the Slovenian economy, we analyse the effectiveness of various categories of public spending and taxes during the period 2020 to 2030, assuming that no crisis occurs. Our simulations show that those public spending measures that entail both demand- and supply-side effects are more effective at stimulating real GDP and increasing employment than pure demand-side measures. This is due to the fact that supply-side measures also increase potential and not only actual GDP. Measures which foster research and development and those which improve the education level of the labour force are particularly effective in this respect. Employment can also be stimulated effectively by cutting the income tax rate and the social security contribution rate, i.e. by reducing the tax wedge on labour income, which positively affects Slovenia's international competitiveness. Successful stabilisation policies should thus contain a supply-side component in addition to a demand-side component. We also provide a first simulation of potential effects of the Covid-19 crisis on the Slovenian economy, which is modelled as a combined demand and supply shock.

The Sun Through Time

Magnetic activity of stars like the Sun evolves in time because of spin-down owing to angular momentum removal by a magnetized stellar wind. These magnetic fields are generated by an internal dynamo driven by convection and differential rotation. Spin-down therefore converges at an age of about 700 Myr for solar-mass stars to values uniquely determined by the stellar mass and age. Before that time, however, rotation periods and their evolution depend on the initial rotation period of a star after it has lost its protostellar/protoplanetary disk. This non-unique rotational evolution implies similar non-unique evolutions for stellar winds and for the stellar high-energy output. I present a summary of evolutionary trends for stellar rotation, stellar wind mass loss and stellar high-energy output based on observations and models.

Runge-Kutta approximation for C 0 -semigroups in the graph norm with applications to time domain boundary integral equations

We consider the approximation of an abstract evolution problem with inhomogeneous side constraint using A-stable Runge-Kutta methods. We derive a priori estimates in norms other than the underlying Banach space. Most notably, we derive estimates in the graph norm of the generator. These results are used to study convolution quadrature based discretizations of a wave scattering and a heat conduction problem.

A proteomic survey of microtubule-associated proteins in a R402H TUBA1A mutant mouse

Microtubules play a critical role in multiple aspects of neurodevelopment, including the generation, migration and differentiation of neurons. A recurrent mutation (R402H) in the α-tubulin gene TUBA1A is known to cause lissencephaly with cerebellar and striatal phenotypes. Previous work has shown that this mutation does not perturb the chaperone-mediated folding of tubulin heterodimers, which are able to assemble and incorporate into the microtubule lattice. To explore the molecular mechanisms that cause the disease state we generated a new conditional mouse line that recapitulates the R402H variant. We show that heterozygous mutants present with laminar phenotypes in the cortex and hippocampus, as well as a reduction in striatal size and cerebellar abnormalities. We demonstrate that homozygous expression of the R402H allele causes neuronal death and exacerbates a cell intrinsic defect in cortical neuronal migration. Microtubule sedimentation assays coupled with quantitative mass spectrometry demonstrated that the binding and/or levels of multiple microtubule associated proteins (MAPs) are perturbed by the R402H mutation including VAPB, REEP1, EZRIN, PRNP and DYNC1l1/2. Consistent with these data we show that the R402H mutation impairs dynein-mediated transport which is associated with a decoupling of the nucleus to the microtubule organising center. Our data support a model whereby the R402H variant is able to fold and incorporate into microtubules, but acts as a gain of function by perturbing the binding of MAPs.

Microtubules are polymers composed of tubulin proteins, which play an important role in the development of the human brain. Genetic mutations in tubulin genes are known to cause neurodevelopmental diseases, including lissencephaly which is characterised by an impairment in the migration of neurons. In this study we investigate how a common mutation (R402H) in TUBA1A causes lissencephaly by generating and characterising a mouse with the same variant. We show that affected animals recapitulate multiple aspects of the human disease; including laminar perturbations in the cortex and hippocampus, attributable to defects in neuronal migration at key developmental time points. To characterize the molecular implications of the R402H mutation we purified microtubules from the developing brain, and analysed the proteins present by mass spectrometry. This revealed that the binding of DYNC1I1/2 to microtubules is altered in mice with the R402H mutation. Our results provide insight into the molecular pathology underlying tubulin related disease states, and provide a foundation for the rational design of therapeutic interventions.

Object manufacture based on a memorized template: Goffin's cockatoos attend to different model features

Although several nonhuman animals have the ability to recognize and match templates in computerized tasks, we know little about their ability to recall and then physically manufacture specific features of mental templates. Across three experiments, Goffin cockatoos (Cacatua goffiniana), a species that can use tools in captivity, were exposed to two pre-made template objects, varying in either colour, size (long or short) or shape (I or L-shaped), where only one template was rewarded. Birds were then given the opportunity to manufacture versions of these objects themselves. We found that all birds carved paper strips from the same colour material as the rewarded template, and half were also able to match the size of a template (long and short). This occurred despite the template being absent at test and birds being rewarded at random. However, we found no evidence that cockatoos could carve L-shaped pieces after learning that L-shaped templates were rewarded, though their manufactured strips were wider than in previous tests. Overall, our results show that Goffin cockatoos possess the ability to physically adjust at least the size dimension of manufactured objects relative to a mental template. This ability has previously only been shown in New Caledonian crows, where template matching was suggested as a potential mechanism allowing for the cumulative cultural transmission of tool designs. Our results show that within avian tool users, the ability to recreate a physical template from memory does not seem to be restricted to species that have cumulative tool cultures.

The Power of Cut-Based Parameters for Computing Edge-Disjoint Paths

This paper revisits the classical edge-disjoint paths (EDP) problem, where one is given an undirected graph G and a set of terminal pairs P and asks whether G contains a set of pairwise edge-disjoint paths connecting every terminal pair in P. Our aim is to identify structural properties (parameters) of graphs which allow the efficient solution of EDP without restricting the placement of terminals in P in any way. In this setting, EDP is known to remain NP-hard even on extremely restricted graph classes, such as graphs with a vertex cover of size 3. We present three results which use edge-separator based parameters to chart new islands of tractability in the complexity landscape of EDP. Our first and main result utilizes the fairly recent structural parameter tree-cut width (a parameter with fundamental ties to graph immersions and graph cuts): we obtain a polynomial-time algorithm for EDP on every graph class of bounded tree-cut width. Our second result shows that EDP parameterized by tree-cut width is unlikely to be fixed-parameter tractable. Our final, third result is a polynomial kernel for EDP parameterized by the size of a minimum feedback edge set in the graph.

Grassland-to-crop conversion in agricultural landscapes has lasting impact on the trait diversity of bees

CONTEXT

Global pollinator decline has motivated much research to understand the underlying mechanisms. Among the multiple pressures threatening pollinators, habitat loss has been suggested as a key-contributing factor. While habitat destruction is often associated with immediate negative impacts, pollinators can also exhibit delayed responses over time.

OBJECTIVES

We used a trait-based approach to investigate how past and current land use at both local and landscape levels impact plant and wild bee communities in grasslands through a functional lens.

METHODS

We measured flower and bee morphological traits that mediate plant-bee trophic linkage in 66 grasslands. Using an extensive database of 20 years of land-use records, we tested the legacy effects of the landscape-level conversion of grassland to crop on flower and bee trait diversity.

RESULTS

Land-use history was a strong driver of flower and bee trait diversity in grasslands. Particularly, bee trait diversity was lower in landscapes where much of the land was converted from grassland to crop long ago. Bee trait diversity was also strongly driven by plant trait diversity computed with flower traits. However, this relationship was not observed in landscapes with a long history of grassland-to-crop conversion. The effects of land-use history on bee communities were as strong as those of current land use, such as grassland or mass-flowering crop cover in the landscape.

CONCLUSIONS

Habitat loss that occurred long ago in agricultural landscapes alters the relationship between plants and bees over time. The retention of permanent grassland sanctuaries within intensive agricultural landscapes can offset bee decline.

Nonlocal-to-Local Convergence of Cahn-Hilliard Equations: Neumann Boundary Conditions and Viscosity Terms

We consider a class of nonlocal viscous Cahn-Hilliard equations with Neumann boundary conditions for the chemical potential. The double-well potential is allowed to be singular (e.g. of logarithmic type), while the singularity of the convolution kernel does not fall in any available existence theory under Neumann boundary conditions. We prove well-posedness for the nonlocal equation in a suitable variational sense. Secondly, we show that the solutions to the nonlocal equation converge to the corresponding solutions to the local equation, as the convolution kernels approximate a Dirac delta. The asymptotic behaviour is analyzed by means of monotone analysis and Gamma convergence results, both when the limiting local Cahn-Hilliard equation is of viscous type and of pure type.

Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel

In spite of many decades of research, the spawning migration of the European eel Anguilla anguilla from the European coast to the Sargasso Sea remains a mystery. In particular, the role of the swimbladder as a buoyancy regulating structure is not yet understood. In this study, we exercised silver eels in a swim tunnel under elevated hydrostatic pressure. The transcriptome of gas gland tissue of these exercised eels was then compared to the known transcriptome of not exercised (control) silver eel gas gland cells. Due to the high infection rate of the eel population with the swimbladder parasite Anguillicola crassus, the comparison also included an exercised group of silver eels with a heavily damaged swimbladder, and we compared the previously published transcriptome of not exercised silver eels with a highly damaged swimbladder with the exercised group of silver eels with a heavily damaged swimbladder. The comparisons of unexercised (control) silver eels with exercised silver eels with functional swimbladder (EF), as well as with exercised silver eels with damaged swimbladder (ED), both showed a significant elevation in transcripts related to glycolytic enzymes. This could also be observed within the comparison of unexercised silver eels with a highly infected swimbladder with exercised eels with a damaged swimbladder (DED). In contrast to EF, in ED a significant elevation in transcript numbers of mitochondrial NADH dehydrogenase was observed. While in EF the transcriptional changes suggested that acid production and secretion was enhanced, in ED these changes appeared to be related to thickened tissue and thus elevated diffusion distances. The remarkable number of differentially expressed transcripts coding for proteins connected to cAMP-dependent signaling pathways indicated that metabolic control in gas gland cells includes cAMP-dependent pathways. In contrast to ED, in EF significant transcriptional changes could be related to the reconstruction of the extracellular matrix, while in ED tissue repair and inflammation was more pronounced. Surprisingly, in exercised eels hypoxia inducible transcription factor expression was elevated. In EF, a large number of genes related to the circadian clock were transcriptionally modified, which may be connected to the circadian vertical migrations observed during the spawning migration.

The biophysical, molecular, and anatomical landscape of pigeon CRY4: A candidate light-based quantal magnetosensor

The biophysical and molecular mechanisms that enable animals to detect magnetic fields are unknown. It has been proposed that birds have a light-dependent magnetic compass that relies on the formation of radical pairs within cryptochrome molecules. Using spectroscopic methods, we show that pigeon cryptochrome clCRY4 is photoreduced efficiently and forms long-lived spin-correlated radical pairs via a tetrad of tryptophan residues. We report that clCRY4 is broadly and stably expressed within the retina but enriched at synapses in the outer plexiform layer in a repetitive manner. A proteomic survey for retinal-specific clCRY4 interactors identified molecules that are involved in receptor signaling, including glutamate receptor-interacting protein 2, which colocalizes with clCRY4. Our data support a model whereby clCRY4 acts as an ultraviolet-blue photoreceptor and/or a light-dependent magnetosensor by modulating glutamatergic synapses between horizontal cells and cones.

The evolution and functional divergence of the histone H2B family in plants

Chromatin regulation of eukaryotic genomes depends on the formation of nucleosome complexes between histone proteins and DNA. Histone variants, which are diversified by sequence or expression pattern, can profoundly alter chromatin properties. While variants in histone H2A and H3 families are well characterized, the extent of diversification of histone H2B proteins is less understood. Here, we report a systematic analysis of the histone H2B family in plants, which have undergone substantial divergence during the evolution of each major group in the plant kingdom. By characterising Arabidopsis H2Bs, we substantiate this diversification and reveal potential functional specialization that parallels the phylogenetic structure of emergent clades in eudicots. In addition, we identify a new class of highly divergent H2B variants, H2B.S, that specifically accumulate during chromatin compaction of dry seed embryos in multiple species of flowering plants. Our findings thus identify unsuspected diverse properties among histone H2B proteins in plants that has manifested into potentially novel groups of histone variants.

In addition to well-studied variants from core histones families H2A and H3, we report that land plants diversified their H2B family, leading to specialized H2B variants with specific patterns of expression, genomic distributions and properties.