The NMR signature of maltose-based glycation in full-length proteins

Reducing sugars can spontaneously react with free amines in protein side chains leading to posttranslational modifications (PTMs) called glycation. In contrast to glycosylation, glycation is a non-enzymatic modification with consequences on the overall charge, solubility, aggregation susceptibility and functionality of a protein. Glycation is a critical quality attribute of therapeutic monoclonal antibodies. In addition to glucose, also disaccharides like maltose can form glycation products. We present here a detailed NMR analysis of the Amadori product formed between proteins and maltose. For better comparison, data collection was done under denaturing conditions using 7 M urea-d4 in D2O. The here presented correlation patterns serve as a signature and can be used to identify maltose-based glycation in any protein that can be denatured. In addition to the model protein BSA, which can be readily glycated, we present data of the biotherapeutic abatacept containing maltose in its formulation buffer. With this contribution, we demonstrate that NMR spectroscopy is an independent method for detecting maltose-based glycation, that is suited for cross-validation with other methods.

How pre-processing decisions affect the reliability and validity of the approach-avoidance task: Evidence from simulations and multiverse analyses with six datasets

Reaction time (RT) data are often pre-processed before analysis by rejecting outliers and errors and aggregating the data. In stimulus-response compatibility paradigms such as the approach-avoidance task (AAT), researchers often decide how to pre-process the data without an empirical basis, leading to the use of methods that may harm data quality. To provide this empirical basis, we investigated how different pre-processing methods affect the reliability and validity of the AAT. Our literature review revealed 108 unique pre-processing pipelines among 163 examined studies. Using empirical datasets, we found that validity and reliability were negatively affected by retaining error trials, by replacing error RTs with the mean RT plus a penalty, and by retaining outliers. In the relevant-feature AAT, bias scores were more reliable and valid if computed with D-scores; medians were less reliable and more unpredictable, while means were also less valid. Simulations revealed bias scores were likely to be less accurate if computed by contrasting a single aggregate of all compatible conditions with that of all incompatible conditions, rather than by contrasting separate averages per condition. We also found that multilevel model random effects were less reliable, valid, and stable, arguing against their use as bias scores. We call upon the field to drop these suboptimal practices to improve the psychometric properties of the AAT. We also call for similar investigations in related RT-based bias measures such as the implicit association task, as their commonly accepted pre-processing practices involve many of the aforementioned discouraged methods. HIGHLIGHTS: • Rejecting RTs deviating more than 2 or 3 SD from the mean gives more reliable and valid results than other outlier rejection methods in empirical data • Removing error trials gives more reliable and valid results than retaining them or replacing them with the block mean and an added penalty • Double-difference scores are more reliable than compatibility scores under most circumstances • More reliable and valid results are obtained both in simulated and real data by using double-difference D-scores, which are obtained by dividing a participant's double mean difference score by the SD of their RTs.

Effects of a dissociative drug on fronto-limbic resting-state functional connectivity in individuals with posttraumatic stress disorder: a randomized controlled pilot study

RATIONALE

A subanesthetic dose of ketamine, a non-competitive N-methyl-D-aspartate glutamate receptor (NMDAR) antagonist, elicits dissociation in individuals with posttraumatic stress disorder (PTSD), who also often suffer from chronic dissociative symptoms in daily life. These debilitating symptoms have not only been linked to worse PTSD trajectories, but also to increased resting-state functional connectivity (RSFC) between medial prefrontal cortex (mPFC) and amygdala, supporting the conceptualization of dissociation as emotion overmodulation. Yet, as studies were observational, causal evidence is lacking.

OBJECTIVES

The present randomized controlled pilot study examines the effect of ketamine, a dissociative drug, on RSFC between mPFC subregions and amygdala in individuals with PTSD.

METHODS

Twenty-six individuals with PTSD received either ketamine (0.5mg/kg; n = 12) or the control drug midazolam (0.045mg/kg; n = 14) during functional magnetic resonance imaging (fMRI). RSFC between amygdala and mPFC subregions, i.e., ventromedial PFC (vmPFC), dorsomedial PFC (dmPFC) and anterior-medial PFC (amPFC), was assessed at baseline and during intravenous drug infusion.

RESULTS

Contrary to pre-registered predictions, ketamine did not promote a greater increase in RSFC between amygdala and mPFC subregions from baseline to infusion compared to midazolam. Instead, ketamine elicited a stronger transient decrease in vmPFC-amygdala RSFC compared to midazolam.

CONCLUSIONS

A dissociative drug did not increase fronto-limbic RSFC in individuals with PTSD. These preliminary experimental findings contrast with prior correlative findings and call for further exploration and, potentially, a more differentiated view on the neurobiological underpinning of dissociative phenomena in PTSD.

Eavesdropping on Tinnitus Using MEG: Lessons Learned and Future Perspectives

Tinnitus has been widely investigated in order to draw conclusions about the underlying causes and altered neural activity in various brain regions. Existing studies have based their work on different tinnitus frameworks, ranging from a more local perspective on the auditory cortex to the inclusion of broader networks and various approaches towards tinnitus perception and distress. Magnetoencephalography (MEG) provides a powerful tool for efficiently investigating tinnitus and aberrant neural activity both spatially and temporally. However, results are inconclusive, and studies are rarely mapped to theoretical frameworks. The purpose of this review was to firstly introduce MEG to interested researchers and secondly provide a synopsis of the current state. We divided recent tinnitus research in MEG into study designs using resting state measurements and studies implementing tone stimulation paradigms. The studies were categorized based on their theoretical foundation, and we outlined shortcomings as well as inconsistencies within the different approaches. Finally, we provided future perspectives on how to benefit more efficiently from the enormous potential of MEG. We suggested novel approaches from a theoretical, conceptual, and methodological point of view to allow future research to obtain a more comprehensive understanding of tinnitus and its underlying processes.

Vibrational entropy of disordering in omphacite

The cations of an ordered omphacite from the Tauern window were gradually disordered in piston cylinder experiments at temperatures between 850 and 1150 °C. The samples were examined by X-ray powder diffraction and then investigated using low-temperature calorimetry and IR spectroscopy. The low-temperature heat capacity data were used to obtain the vibrational entropies, and the line broadening of the IR spectra served as a tool to investigate the disordering enthalpy. These data were then used to calculate the configurational entropy as a function of temperature. The vibrational entropy does not change during the cation ordering phase transition from space group C2/c to P2/n at 865 °C but increases with a further temperature increase due to the reduction of short-range order.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00269-023-01260-7.

Effect of temporary freezing on postmortem protein degradation patterns

BACKGROUND

A precise determination of time since death plays a major role in forensic routine. Currently available techniques for estimating the postmortem interval (PMI) are restricted to specific time periods or cannot be applied for individual case-specific reasons. During recent years, it has been repeatedly demonstrated that Western blot analysis of postmortem muscle protein degradation can substantially contribute to overcome these limitations in cases with different background. Enabling to delimit time points at which certain marker proteins undergo distinct degradation events, the method has become a reasonable new tool for PMI delimitation under various forensic scenarios. However, additional research is yet required to improve our understanding of protein decomposition and how it is affected by intrinsic and extrinsic factors. Since there are temperature limits for proteolysis, and investigators are confronted with frozen corpses, investigation of the effects of freezing and thawing on postmortem protein decomposition in the muscle tissue is an important objective to firmly establish the new method. It is also important because freezing is often the only practical means to intermittently preserve tissue samples from both true cases and animal model research.

METHODS

Sets of dismembered pig hind limbs, either freshly detached non-frozen, or thawed after 4 months of freeze-storage (n = 6 each), were left to decompose under controlled conditions at 30 °C for 7 days and 10 days, respectively. Samples of the M. biceps femoris were regularly collected at predefined time points. All samples were processed via SDS-PAGE and Western blotting to identify the degradation patterns of previously characterized muscle proteins.

RESULTS

Western blots show that the proteins degrade predictably over time in precise patterns that are largely unaffected by the freeze-and-thaw process. Investigated proteins showed complete degradation of the native protein band, partly giving rise to degradation products present in distinct time phases of the decomposition process.

CONCLUSION

This study provides substantial new information from a porcine model to assess the degree of bias that freezing and thawing induces on postmortem degradation of skeletal muscle proteins. Results support that a freeze-thaw cycle with prolonged storage in frozen state has no significant impact on the decomposition behavior. This will help to equip the protein degradation-based method for PMI determination with a robust applicability in the normal forensic setting.

Emotional eating: elusive or evident? Integrating laboratory, psychometric and daily life measures

PURPOSE

Emotional eating (EE) refers to eating in response to (negative) emotions. Evidence for the validity of EE is mixed: some meta-analyses find EE only in eating disordered patients, others only in restrained eaters, which suggest that only certain subgroups show EE. Furthermore, EE measures from lab-based assessments, ecological momentary assessment (EMA), and psychometric measures often diverge. This paper tested whether the covariance of these three different EE methods can be modeled through a single latent variable (factorial validity), and if so, how this variable would relate to restrained eating (construct validity), Body-Mass-Index (BMI), and subclinical eating disorder symptomatology (concurrent validity).

METHODS

102 non-eating disordered female participants with a wide BMI range completed EE measures from three methods: psychometric questionnaires, a laboratory experiment (craving ratings of food images in induced neutral vs. negative emotion) and EMA questionnaires (within-participant correlations of momentary negative emotions and momentary food cravings across 9 days). Two measures for each method were extracted and submitted to confirmatory factor analysis.

RESULTS

A one-factor model provided a good fit. The resulting EElat factor correlated positively with subclinical eating disorder symptoms and BMI but not with restrained eating.

CONCLUSIONS

The one-factor solution shows that the EE construct can validly be assessed with three different methods. Individual differences in EE are supported by the data and are related to eating and weight problem symptomatology but not to restrained eating. This supports learning accounts of EE and underscores the relevance of the EE construct to physical and mental health.

LEVEL OF EVIDENCE

II (Evidence obtained from well-designed controlled trials without randomization).

Blood-Based Biomarkers for Managing Workload in Athletes: Considerations and Recommendations for Evidence-Based Use of Established Biomarkers

Blood-based biomarkers can provide an objective individualized measure of training load, recovery, and health status in order to reduce injury risk and maximize performance. Despite enormous potentials, especially owing to currently evolving technology, such as point-of-care testing, and advantages, in terms of objectivity and non-interference with the training process, there are several pitfalls in the use and interpretation of biomarkers. Confounding variables such as preanalytical conditions, inter-individual differences, or an individual chronic workload can lead to variance in resting levels. In addition, statistical considerations such as the detection of meaningful minimal changes are often neglected. The lack of generally applicable and individual reference levels further complicates the interpretation of level changes and thus load management via biomarkers. Here, the potentials and pitfalls of blood-based biomarkers are described, followed by an overview of established biomarkers currently used to support workload management. Creatine kinase is discussed in terms of its evidence for workload management to illustrate the limited applicability of established markers for workload management to date. We conclude with recommendations for best practices in the use and interpretation of biomarkers in a sport-specific context.

Unambiguous Identification of Glucose-Induced Glycation in mAbs and other Proteins by NMR Spectroscopy

OBJECTIVE

Glycation is a non-enzymatic and spontaneous post-translational modification (PTM) generated by the reaction between reducing sugars and primary amine groups within proteins. Because glycation can alter the properties of proteins, it is a critical quality attribute of therapeutic monoclonal antibodies (mAbs) and should therefore be carefully monitored. The most abundant product of glycation is formed by glucose and lysine side chains resulting in fructoselysine after Amadori rearrangement. In proteomics, which routinely uses a combination of chromatography and mass spectrometry to analyze PTMs, there is no straight-forward way to distinguish between glycation products of a reducing monosaccharide and an additional hexose within a glycan, since both lead to a mass difference of 162 Da.

METHODS

To verify that the observed mass change is indeed a glycation product, we developed an approach based on 2D NMR spectroscopy spectroscopy and full-length protein samples denatured using high concentrations of deuterated urea.

RESULTS

The dominating β-pyranose form of the Amadori product shows a characteristic chemical shift correlation pattern in 1H-13C HSQC spectra suited to identify glucose-induced glycation. The same pattern was observed in spectra of a variety of artificially glycated proteins, including two mAbs, as well as natural proteins.

CONCLUSION

Based on this unique correlation pattern, 2D NMR spectroscopy can be used to unambiguously identify glucose-induced glycation in any protein of interest. We provide a robust method that is orthogonal to MS-based methods and can also be used for cross-validation.

"It's where learning and teaching begins ‒ is this relationship" - insights on the teacher-student relationship at university from the teachers' perspective

Positive teacher-student relationships have been identified as important for teacher and student well-being and for high-quality teaching and learning processes and outcomes. However, research on the perceptions of teachers in higher education on a high-quality relationship with students and the perceived antecedents is still scarce. This study aimed to address this research gap by interviewing 15 Australian higher education teachers about their perception of forming relationships with first-year students. The results suggest that the quality of the teacher-student relationship comprises both a professional and an interpersonal dimension, reflecting the different roles teachers and students assume within it. These two dimensions can be further differentiated into various relational quality indicators, such as approachability, care, support, trust, and others. Furthermore, the results indicate that several contextual and personal attributes contribute to the development of this relationship. Implications about how to shape positive relationships between teachers and students in higher education are discussed.

Dating of polyhalite: a difficult 40Ar/39Ar dating tool of diagenetic to very low-grade metamorphic processes

Halite already deforms at surface temperatures. A valuable universal dating tool to constrain the timing of sedimentary, diagenetic, or deformational structures is still missing. The evaporite mineral polyhalite can be dated by the ⁴⁰Ar/³⁹Ar method. On the example of the extremely deformed halite deposits of the Eastern Alps, polyhalite was tested to date early diagenetic stages of the deposits. The sedimentological investigation of the present study indicates that some of the macrostructures of polyhalite had a syn-depositional origin during the late Permian. It is supposed that polyhalite originated during reflux of brines. All samples selected for age dating represent characteristic microfabric types of euhedral to subhedral polyhalite crystals. Intact macro- and non-recrystallized looking microstructures of polyhalite can be expected to give plateau ages. However, nearly all measurements produced overdispersed data that do not define an age. The oldest age steps thus represent only minimum ages. A closer look revealed grain boundary migration, subgrain rotation recrystallization, twinning, and fluid-supported grain size increase. These recovery processes obscured the original ages and/or reflect the origin of new polyhalite in place of the original individuals. Based on these microstructures, the age data are supposed to reflect the circulation of aqueous fluids. Just extremely careful separation of individual crystals or in situ age dating under the microscope will be successful in dating polyhalite. Nevertheless, polyhalite can potentially serve to date deformational events of halite deposits due to its easy recrystallization property.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00531-022-02219-9.

Galactose induces formation of cell wall stubs and cell death in Arabidopsis roots

Arabidopsis seedlings growing on low concentration of galactose stop regular root growth. Incomplete cell division with cell wall stubs, binuclear and giant cells and lignified root tips are observed. Galactose is a sugar abundant in root cell walls of Arabidopsis. Nevertheless, we found that the germination of Arabidopsis seedlings on galactose containing media causes a strong modification of the root development, as shown by analysing the root with microscopy methods ranging from the bright field over confocal to transmission electron microscopy. At concentrations of about 1 mM, the growth of the primary root stops after a few days though stem cell markers like WOX5 are still expressed. The root tip swells and forms a slightly opaque, partially lignified structure in parts of the cortex and the central cylinder. The formation of the cell plate after mitosis is impaired, often leading to cell wall stubs and binuclear cells. Some cells in the cortex and the central cylinder degenerate, while some rhizodermal and cortical cells increase massively in size. The galactose toxicity phenotype in Arabidopsis depends on the activity of galactokinase and is completely diminished in galactokinase knock-out lines. From the comparison of the galactose toxicity phenotype with those of cytokinesis mutants and plants treated with appropriate inhibitors we speculate that the toxicity syndrome of galactose is caused by interference with intracellular vesicle transport or cell wall biogenesis.

Excess heat capacity and entropy of mixing along the hydroxyapatite-chlorapatite and hydroxyapatite-fluorapatite binaries

The heat capacity, C _p, of synthetic hydroxyapatite [Ca₅(PO₄)₃OH-OH-Ap], as well as of ten compositions along the OH-Ap-chlorapatite (Cl-Ap) join and 12 compositions along the OH-Ap-fluorapatite (F-Ap) join have been measured using relaxation calorimetry (heat capacity option of the Physical Properties Measurement System-PPMS) and differential scanning calorimetry (DSC) in the temperature range of 5-764 K. Apatites along the Cl-OH and F-OH joins were synthesized at 1100 °C and 300 MPa in an internally heated gas pressure vessel via an exchange process between synthetic fluorapatite or chlorapatite crystals (200-500 μm size) and a series of Ca(OH)₂-H₂O solutions with specific compositions and amounts relative to the starting apatite. The standard third-law entropy of OH-Ap, derived from the low-temperature heat capacity measurements, is S° = 386.3 ± 2.5 J mol^-1 K^-1, which is ~ 1% lower than that resulting from low-temperature adiabatic calorimetry data on OH-Ap from the 1950's. The heat capacity of OH-Ap above 298.15 K shows a hump-shaped anomaly centred around 442 K. Based on published structural and calorimetric work, this feature is interpreted to result from a monoclinic to hexagonal phase transition. Super ambient C _p up to this transition can be represented by the polynomial: C p OH - Ap 298 K - 442 K J mol - 1 K - 1 = 1013.7 - 13735.5 T - 0.5 + 2.616718 10 7 T - 2 - 3.551381 10 9 T - 3 . . The DSC data above this transition were combined with heat capacities computed using density functional theory and can be given by the C _p polynomial: C p OH - Ap > 442 K J mol - 1 K - 1 = 877.2 - 11393.7 T - 0.5 + 5.452030 10 7 T - 2 - 1.394125 10 10 T - 3 . Positive excess heat capacities of mixing, ∆C _p ^ex, in the order of 1-2 J mol^-1 K^-1, occur in both solid solutions at around 70 K. They are significant at these conditions exceeding the 2σ-uncertainty of the data. This positive ∆C _p ^ex is compensated by a negative ∆C _p ^ex of the same order at around 250 K in both binaries. At higher temperatures (up to 1200 K), ∆C _p ^ex is zero within error for all solid solution members. As a consequence, the calorimetric entropies, S_cal, show no deviation from ideal mixing behaviour within a 2σ-uncertainty for both joins. Excess entropies of mixing, ∆S^ex, are thus zero for the OH-Ap-F-Ap, as well as for the OH-Ap-Cl-Ap join. The C _p-T behaviour of the OH-Ap endmember is discussed in relation to that of the F- and Cl-endmembers.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00269-021-01167-1.

Animal reservoirs of SARS-CoV-2: calculable COVID-19 risk for older adults from animal to human transmission

The current COVID-19 pandemic, caused by the highly contagious respiratory pathogen SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has already claimed close to three million lives. SARS-CoV-2 is a zoonotic disease: it emerged from a bat reservoir and it can infect a number of agricultural and companion animal species. SARS-CoV-2 can cause respiratory and intestinal infections, and potentially systemic multi-organ disease, in both humans and animals. The risk for severe illness and death with COVID-19 significantly increases with age, with older adults at highest risk. To combat the pandemic and protect the most susceptible group of older adults, understanding the human-animal interface and its relevance to disease transmission is vitally important. Currently high infection numbers are being sustained via human-to-human transmission of SARS-CoV-2. Yet, identifying potential animal reservoirs and potential vectors of the disease will contribute to stronger risk assessment strategies. In this review, the current information about SARS-CoV-2 infection in animals and the potential spread of SARS-CoV-2 to humans through contact with domestic animals (including dogs, cats, ferrets, hamsters), agricultural animals (e.g., farmed minks), laboratory animals, wild animals (e.g., deer mice), and zoo animals (felines, non-human primates) are discussed with a special focus on reducing mortality in older adults.

A heterodox defense of the actualist higher-order thought theory

I defend the actualist higher-order thought theory against four objections. The first objection contends that the theory is circular. The second one contends that the theory is unable to account for the alleged epistemic position we are in with respect to our own conscious mental states. The third one contends that the theory is unable to account for the evidence we have for the proposition that all conscious mental states are represented. The fourth one contends that the theory does not accommodate the intimacy we have with our own conscious mental states. To some extent, my defense will be heterodox, in the sense that I will show that some objections are satisfactorily answerable even if we concede to the objectors a point that higher-order theorists do not seem to be willing to concede, that is, that the theory is the result of conceptual analysis.

Effective Connectivity of the Hippocampus Can Differentiate Patients with Schizophrenia from Healthy Controls: A Spectral DCM Approach

We applied spectral dynamic causal modelling (Friston et al. in Neuroimage 94:396–407. 10.1016/j.neuroimage.2013.12.009, 2014) to analyze the effective connectivity differences between the nodes of three resting state networks (i.e. default mode network, salience network and dorsal attention network) in a dataset of 31 male healthy controls (HC) and 25 male patients with a diagnosis of schizophrenia (SZ). Patients showed increased directed connectivity from the left hippocampus (LHC) to the: dorsal anterior cingulate cortex (DACC), right anterior insula (RAI), left frontal eye fields and the bilateral inferior parietal sulcus (LIPS & RIPS), as well as increased connectivity from the right hippocampus (RHC) to the: bilateral anterior insula (LAI & RAI), right frontal eye fields and RIPS. In SZ, negative symptoms predicted the connectivity strengths from the LHC to: the DACC, the left inferior parietal sulcus (LIPAR) and the RHC, while positive symptoms predicted the connectivity strengths from the LHC to the LIPAR and from the RHC to the LHC. These results reinforce the crucial role of hippocampus dysconnectivity in SZ pathology and its potential as a biomarker of disease severity.

Speeding Up Reachability Queries in Public Transport Networks Using Graph Partitioning

Computing path queries such as the shortest path in public transport networks is challenging because the path costs between nodes change over time. A reachability query from a node at a given start time on such a network retrieves all points of interest (POIs) that are reachable within a given cost budget. Reachability queries are essential building blocks in many applications, for example, group recommendations, ranking spatial queries, or geomarketing. We propose an efficient solution for reachability queries in public transport networks. Currently, there are two options to solve reachability queries. (1) Execute a modified version of Dijkstra's algorithm that supports time-dependent edge traversal costs; this solution is slow since it must expand edge by edge and does not use an index. (2) Issue a separate path query for each single POI, i.e., a single reachability query requires answering many path queries. None of these solutions scales to large networks with many POIs. We propose a novel and lightweight reachability index. The key idea is to partition the network into cells. Then, in contrast to other approaches, we expand the network cell by cell. Empirical evaluations on synthetic and real-world networks confirm the efficiency and the effectiveness of our index-based reachability query solution.

[Students' perspectives on school and daily life in times of the Corona crisis in early 2020]

The aim of the international study "Futures Literacy-Children's Crisis Narrations as Spaces of Utopias of Solidarity" is to gain insights into their (living) world and perspectives on home-schooling in times of the Corona Crisis by means of crisis narratives by schoolchildren. The data collection (n = 237) is based on a special writing assignment to the pupils, in which they are asked to describe how they tell their grandchildren about the time of the Corona crisis in the fictional future in the role of the grandparents-60 years later. The task requires an anticipatory effort from the present point of view, which stimulates them to reflect on their current situation from a certain "distance" (stimulating them to adopt a perspective and to construct a "vision"). The perspective of children is explicitly placed in the center of interest in order to draw conclusions about the issues that concern this age group in times of crisis. The aim is to find out how pupils from different European countries (Switzerland, Austria and Greece) deal with the Corona crisis and its consequences for their life-world, how they experience it and how they process it cognitively/emotionally. Theoretically, the study ties in with the concept of futures literacy. The texts produced by the students will be evaluated by means of a systematic combination of quantitative and qualitative content analysis (using Latent Class Analysis). Typical narrative and argumentative text patterns (narrative characteristics) will be identified.

A radical relationist solution to the problem of intentional inexistence

The problem of intentional inexistence arises because the following (alleged) intuitions are mutually conflicting: it seems that sometimes we think about things that do not exist; it seems that intentionality is a relation between a thinker and what such a thinker thinks about; it seems that relations entail the existence of what they relate. In this paper, I argue for what I call a radical relationist solution. First, I contend that the extant arguments for the view that relations entail the existence of their relata are wanting. In this regard, I defend a kind of pluralism about relations according to which more than one kind of relation involves non-existents. Second, I contend that there are reasons to maintain that all thoughts are relations between thinkers and the things they are about. More accurately, I contend that the radical relationist solution is to be preferred to both the intentional content solution (as developed by Crane) and the adverbial property solution (as developed by Kriegel). Finally, I argue that once the distinction between thinking "X" and thinking about X has been drawn, the radical relationist solution can handle issues like ontological commitment, substitutivity failure, scrutability, and non-specificity.

Detecting aspartate isomerization and backbone cleavage after aspartate in intact proteins by NMR spectroscopy

The monitoring of non-enzymatic post-translational modifications (PTMs) in therapeutic proteins is important to ensure drug safety and efficacy. Together with methionine and asparagine, aspartic acid (Asp) is very sensitive to spontaneous alterations. In particular, Asp residues can undergo isomerization and peptide-bond hydrolysis, especially when embedded in sequence motifs that are prone to succinimide formation or when followed by proline (Pro). As Asp and isoAsp have the same mass, and the Asp-Pro peptide-bond cleavage may lead to an unspecific mass difference of + 18 Da under native conditions or in the case of disulfide-bridged cleavage products, it is challenging to directly detect and characterize such modifications by mass spectrometry (MS). Here we propose a 2D NMR-based approach for the unambiguous identification of isoAsp and the products of Asp-Pro peptide-bond cleavage, namely N-terminal Pro and C-terminal Asp, and demonstrate its applicability to proteins including a therapeutic monoclonal antibody (mAb). To choose the ideal pH conditions under which the NMR signals of isoAsp and C-terminal Asp are distinct from other random coil signals, we determined the pK_a values of isoAsp and C-terminal Asp in short peptides. The characteristic ¹H-¹³C chemical shift correlations of isoAsp, N-terminal Pro and C-terminal Asp under standardized conditions were used to identify these PTMs in lysozyme and in the therapeutic mAb rituximab (MabThera) upon prolonged storage under acidic conditions (pH 4-5) and 40 °C. The results show that the application of our 2D NMR-based protocol is straightforward and allows detecting chemical changes of proteins that may be otherwise unnoticed with other analytical methods.

Does spatiotemporal nutrient variation allow more species to coexist?

Temporal heterogeneity in nutrient availability is known to increase phytoplankton diversity by allowing more species to coexist under different resource niches. Spatial heterogeneity has also been positively correlated with species diversity. Here we investigated how temporal and spatial differences in nutrient addition together impact biodiversity in metacommunities varying in the degree of connectivity among the patches. We used a microcosm experimental design to test two spatiotemporal ways of supplying nutrients: synchronously (nutrients were added regionally-to all four patches at the same time) and asynchronously (nutrients were added locally-to a different patch each time), combined with two different degrees of connectivity among the patches (low or high connectivity). We used three species of algae and one species of cyanobacteria as the primary producers; and five ciliate and two rotifer species as the grazers. We expected higher diversity in metacommunities receiving an asynchronous nutrient supply, assuming stronger development of heterogeneous patches with this condition rather than with synchronous nutrient supply. This result was expected, however, to be dependent on the degree of connectivity among patches. We found significant effects of nutrient addition in both groups of organisms. Phytoplankton diversity increased until the fourth week (transiently) and zooplankton richness was persistently higher under asynchronous nutrient addition. Our results were consistent with our hypothesis that asynchronicity in nutrient supply would create a more favorable condition for species to co-occur. However, this effect was, in part, transient and was not influenced by the degree of connectivity.

A Critical Examination of the Practical Implications Derived from the Food Addiction Concept

PURPOSE OF REVIEW

Adopting an addiction perspective on eating disorders and obesity may have practical implications for diagnostic classification, prevention, and treatment of these disorders. The present article critically examines these implications derived from the food addiction concept.

RECENT FINDINGS

Introducing food addiction as a new disorder in diagnostic classification system seems redundant as most individuals with an addiction-like eating behavior are already covered by established eating disorder diagnoses. Food addiction may be a useful metaphor in the treatment of binge eating, but would be inappropriate for the majority of obese individuals. Implying an addiction to certain foods is not necessary when applying certain approaches inspired by the addiction field for prevention and treatment of obesity. The usefulness of abstinence models in the treatment of eating disorders and obesity needs to be rigorously tested in future studies. Some practical implications derived from the food addiction concept provide promising avenues for future research (e.g., using an addiction framework in the treatment of binge eating or applying abstinence models). For others, however, the necessity of implying an addiction to some foods needs to be scrutinized.

Does altered protein metabolism interfere with postmortem degradation analysis for PMI estimation?

An accurate estimation of the postmortem interval (PMI) is a central aspect in forensic routine. Recently, a novel approach based on the analysis of postmortem muscle protein degradation has been proposed. However, a number of questions remain to be answered until sensible application of this method to a broad variety of forensic cases is possible. To evaluate whether altered in vivo protein metabolism interferes with postmortem degradation patterns, we conducted a comparative study. We developed a standardized animal degradation model in rats, and collected additional muscle samples from animals recovering from muscle injury and from rats with developed disuse muscle atrophy after induced spinal cord injury. All samples were analyzed by SDS-PAGE and Western blot, labeling well-characterized muscle proteins. Tropomyosin was found to be stable throughout the investigated PMI and no alterations were detected in regenerating and atrophic muscles. In contrast, significant predictable postmortem changes occurred in desmin and vinculin protein band patterns. While no significant deviations from native patterns were detected in at-death samples of disuse muscle atrophy, interestingly, samples of rats recovering from muscle injury revealed additional desmin and vinculin degradation bands that did not occur in this form in any of the examined postmortem samples regardless of PMI. It remains to be investigated whether in vivo-altered metabolism influences postmortem degradation kinetics or if such muscle samples undergo postmortem degradation in a regular fashion.

Are animal models predictive for human postmortem muscle protein degradation?

A most precise determination of the postmortem interval (PMI) is a crucial aspect in forensic casework. Although there are diverse approaches available to date, the high heterogeneity of cases together with the respective postmortal changes often limit the validity and sufficiency of many methods. Recently, a novel approach for time since death estimation by the analysis of postmortal changes of muscle proteins was proposed. It is however necessary to improve the reliability and accuracy, especially by analysis of possible influencing factors on protein degradation. This is ideally investigated on standardized animal models that, however, require legitimization by a comparison of human and animal tissue, and in this specific case of protein degradation profiles. Only if protein degradation events occur in comparable fashion within different species, respective findings can sufficiently be transferred from the animal model to application in humans. Therefor samples from two frequently used animal models (mouse and pig), as well as forensic cases with representative protein profiles of highly differing PMIs were analyzed. Despite physical and physiological differences between species, western blot analysis revealed similar patterns in most of the investigated proteins. Even most degradation events occurred in comparable fashion. In some other aspects, however, human and animal profiles depicted distinct differences. The results of this experimental series clearly indicate the huge importance of comparative studies, whenever animal models are considered. Although animal models could be shown to reflect the basic principles of protein degradation processes in humans, we also gained insight in the difficulties and limitations of the applicability of the developed methodology in different mammalian species regarding protein specificity and methodic functionality.

Three Kinds of Nonconceptual Seeing-as

It is commonly supposed that perceptual representations in some way embed concepts and that this embedding accounts for the phenomenon of seeing-as. But there are good reasons, which will be reviewed here, to doubt that perceptions embed concepts. The alternative is to suppose that perceptions are marks in a perceptual similarity space that map into locations in an objective quality space. From this point of view, there are at least three sorts of seeing-as. First, in cases of ambiguity resolution (such as the duck-rabbit), the schematicity of the figure leaves us with a choice as to where in perceptual similarity space to place a mark (closer to the marks that represent rabbits or closer to the marks that represent ducks). Second, in cases where expertise affects perception (as when, for example, we learn to distinguish various kinds of tree leaves), the accumulation of perceptual landmarks permits a more precise placement of a mark in perceptual similarity space. Third, extensive experience with an object (e.g., the family dog) allows similarity to that object to serve as an acquired dimension in perceptual similarity space, which in turn affects the relative similarities of other objects.

First application of a protein-based approach for time since death estimation

Awareness of postmortem degradation processes in a human body is fundamental to develop methods for forensic time since death estimation (TDE). Currently, applied approaches are all more or less limited to certain postmortem phases, or have restrictions on behalf of circumstances of death. Novel techniques, however, rarely exceed basic research phases due to various reasons. We report the first application of a novel method, based on decay of muscle proteins, in a recent case of murder-suicide, where other TDE methods failed to obtain data. We detected considerably different protein degradation profiles in both individuals involved and compared the data to our presently available database. We obtained statistical evidence for un-simultaneous death and therefore received valuable information to trace the progression of events based on protein degradation. Although we could not sensibly convert the data to respective times of death, this case highlights the potential for future application and elucidates the necessary further steps to develop a viable TDE method.

Water ascent in trees and lianas: the cohesion-tension theory revisited in the wake of Otto Renner

The cohesion-tension theory of water ascent (C-T) has been challenged over the past decades by a large body of experimental evidence obtained by means of several minimum or non-invasive techniques. The evidence strongly suggests that land plants acquire water through interplay of several mechanisms covered by the multi-force theory of (U. Zimmermann et al. New Phytologist 162: 575-615, 2004). The diversity of mechanisms includes, for instance, water acquisition by inverse transpiration and thermodynamically uphill transmembrane water secretion by cation-chloride cotransporters (L.H. Wegner, Progress in Botany 76:109-141, 2014). This whole plant perspective was opened by Otto Renner at the beginning of the last century who supported experimentally the strictly xylem-bound C-T mechanism, yet anticipated that the water ascent involves both the xylem conduit and parenchyma tissues. The survey also illustrates the known paradigm that new techniques generate new insights, as well as a paradigm experienced by Max Planck that a new scientific idea is not welcomed by the community instantly.