Structural diversity in integrin/talin interactions

The adhesion of integrins to the extracellular matrix is regulated by binding of the cytoskeletal protein talin to the cytoplasmic tail of the β-integrin subunit. Structural studies of this interaction have hitherto largely focused on the β3-integrin, one member of the large and diverse integrin family. Here, we employ NMR to probe interactions and dynamics, revealing marked structural diversity in the contacts between β1A, β1D, and β3 tails and the Talin1 and Talin2 isoforms. Coupled with analysis of recent structures of talin/β tail complexes, these studies elucidate the thermodynamic determinants of this heterogeneity and explain why the Talin2/β1D isoforms, which are co-localized in striated muscle, form an unusually tight interaction. We also show that talin/integrin affinity can be enhanced 1000-fold by deleting two residues in the β tail. Together, these studies illustrate how the integrin/talin interaction has been fine-tuned to meet varying biological requirements.     

Analysis of Jmjd6 cellular localization and testing for its involvement in histone demethylation

Background

Methylation of residues in histone tails is part of a network that regulates gene expression. JmjC domain containing proteins catalyze the oxidative removal of methyl groups on histone lysine residues. Here, we report studies to test the involvement of Jumonji domain-containing protein 6 (Jmjd6) in histone lysine demethylation. Jmjd6 has recently been shown to hydroxylate RNA splicing factors and is known to be essential for the differentiation of multiple tissues and cells during embryogenesis. However, there have been conflicting reports as to whether Jmjd6 is a histone-modifying enzyme.

Methodology/Principal Findings

Immunolocalization studies reveal that Jmjd6 is distributed throughout the nucleoplasm outside of regions containing heterochromatic DNA, with occasional localization in nucleoli. During mitosis, Jmjd6 is excluded from the nucleus and reappears in the telophase of the cell cycle. Western blot analyses confirmed that Jmjd6 forms homo-multimers of different molecular weights in the nucleus and cytoplasm. A comparison of mono-, di-, and tri-methylation states of H3K4, H3K9, H3K27, H3K36, and H4K20 histone residues in wildtype and Jmjd6-knockout cells indicate that Jmjd6 is not involved in the demethylation of these histone lysine residues. This is further supported by overexpression of enzymatically active and inactive forms of Jmjd6 and subsequent analysis of histone methylation patterns by immunocytochemistry and western blot analysis. Finally, treatment of cells with RNase A and DNase I indicate that Jmjd6 may preferentially associate with RNA/RNA complexes and less likely with chromatin.

Conclusions/Significance

Taken together, our results provide further evidence that Jmjd6 is unlikely to be involved in histone lysine demethylation. We confirmed that Jmjd6 forms multimers and showed that nuclear localization of the protein involves association with a nucleic acid matrix.     

Evaluating support for the current classification of eukaryotic diversity

Perspectives on the classification of eukaryotic diversity have changed rapidly in recent years, as the four eukaryotic groups within the five-kingdom classification--plants, animals, fungi, and protists--have been transformed through numerous permutations into the current system of six "supergroups." The intent of the supergroup classification system is to unite microbial and macroscopic eukaryotes based on phylogenetic inference. This supergroup approach is increasing in popularity in the literature and is appearing in introductory biology textbooks. We evaluate the stability and support for the current six-supergroup classification of eukaryotes based on molecular genealogies. We assess three aspects of each supergroup: (1) the stability of its taxonomy, (2) the support for monophyly (single evolutionary origin) in molecular analyses targeting a supergroup, and (3) the support for monophyly when a supergroup is included as an out-group in phylogenetic studies targeting other taxa. Our analysis demonstrates that supergroup taxonomies are unstable and that support for groups varies tremendously, indicating that the current classification scheme of eukaryotes is likely premature. We highlight several trends contributing to the instability and discuss the requirements for establishing robust clades within the eukaryotic tree of life.     

A comprehensive approach to visual and functional assessment of experimental vascular lesions in vivo

The role of metabolic factors derived from cardiac muscle in the development of reactive hyperemia after brief occlusions of the coronary circulation seems to be well established. However, the contribution of occlusion-induced changes in hemodynamic forces to eliciting reactive hyperemia is less known. We hypothesized that in isolated coronary arterioles changes in intraluminal pressure and flow, during and after release of occlusion (O/R), themselves via activating intrinsic mechanosensitive mechanisms, elicit release of vasoactive factors resulting in reactive dilations. Thus in isolated coronary arterioles (diameter: 88 +/- 8 microm) changes in diameter to changes in pressure or pressure plus flow (P+F) during and after a brief period (30, 60, and 120 s) of O/R of cannulating tube were measured by videomicroscopy. In response to both types of O/R, diameter first decreased, then, subsequently increased during occlusions. When only pressure was changed (from 80-10-80 mmHg), after release of occlusion, peak dilations increased as a function of the duration of occlusions. After flow was established (30 microl/min), O/R elicited changes in both pressure and flow (from 80-10-80 mmHg and from 0 to 30 microl/min). In these conditions, after the release of occlusions, not only the peak but also the duration of reactive dilation increased significantly as a function of the length of occlusions. The dilations during, and peak dilations after occlusions both in pressure and P+F protocols were significantly reduced by the inhibition of NO synthase with Nomega-nitro-L-arginine-methyl-ester (L-NAME) or by endothelium removal, whereas duration of postocclusion dilations were reduced by L-NAME or by endothelium removal only in P+F protocols. Furthermore, in both protocols, catalase significantly reduced the peak but not the duration of reactive dilations. Thus, mechanosensitive mechanisms that are sensitive to deformation, pressure, stretch, and wall shear stress elicit release of NO and H2O2, resulting in reactive dilation of isolated coronary arterioles.     

Improved fluorogenic histone deacetylase assay for high-throughput-screening applications

Histone deacetylases (HDACs) are key targets for chemotherapeutic intervention in malignant diseases. In this paper, a highly sensitive, nonisotopic, homogeneous assay for high-throughput screening of HDAC inhibitors is presented. The assay is based on a new fluorogenic peptidic substrate of HDACs comprising an epsilon-acetylated lysyl moiety and an adjacent 4-methylcoumarin-7-amide moiety at the C terminus of the peptide chain. Upon deacetylation of the acetylated lysyl moiety, molecules are recognized as substrates by trypsin, which releases highly fluorescent 7-amino-4-methylcoumarin molecules in a subsequent step of the assay. The fluorescence increase is directly proportional to the amount of deacetylated substrate molecules, i.e., HDAC activity. Validation of an improved version of the assay revealed (i) a significantly lower enzyme consumption, (ii) an increased screening window coefficient, (iii) a good tolerance toward organic solvents, and (iv) a good suitability for a whole range of different HDAC-like enzymes. The novel assay thus will expedite studies of HDAC-like enzymes and in vitro screening for drug discovery.     

Energy metabolism and metabolic rate of the alder leaf beetle Agelastica alni (L.) (Coleoptera,Chrysomelidae) under aerobic and anaerobic conditions: a microcalorimetric study

In early fall, adult alder leaf beetles (Agelastica alni L.) retreat, for overwintering, to the top layer of the soil near their forage trees where the ground gets easily waterlogged so that the beetles will be submerged and cut off from atmospheric oxygen. Hence, unlike most other adult insects, alder leaf beetles encounter hypoxia/anoxia in their natural habitat and this may occur at moderate temperature. Exposing beetles to pure nitrogen gas at 20 degrees C had similar behavioral and metabolic effects as submerging them in water, causing rapid immobility and increasing the content of lactate about sevenfold to some 5&mgr;molg(-1) body weight during 10h anoxia. Recovery from 10 h hypoxia/anoxia in pure nitrogen was complete within about 90min.Hypoxia/anoxia triggered a marked decrease in metabolic activity in the beetles (microcalorimetry at 21.7 degrees C) as indicated by a precipitous drop in their heat flow rate, from 1.39+/-0.27 to 0.08+/-0.04mWg(-1) body weight, i.e. by about 94%, when the flow of gas through the calorimeter was switched from air to pure nitrogen. Post-anoxic recovery was accompanied by a peak in heat flow rate that exceeded the basal normoxic rate by about 50%. The homoeostasis of adenine nucleotides in Agelastica is lost when oxygen is wanting. Submergence at 15 degrees C for three days caused a dramatic fall in ATP, to less than 2% of the normoxic value, and a marked increase in AMP, while the total contents of adenine nucleotides decreased by almost two-thirds. Reduced metabolic activity, combined with the capacity to regenerate ATP after readmission of air, is regarded as a key factor for surviving transient lack of oxygen in alder leaf beetles.     

Cell adhesion monitoring using a quartz crystal microbalance: comparative analysis of different mammalian cell lines

The quartz crystal microbalance (QCM) has been widely accepted as a sensitive technique to follow adsorption processes in gas as well as in liquid environments. However, there are only a few reports about the use of this technique to monitor the attachment and spreading of mammalian cells onto a solid support in culture. Using a QCM-setup we investigated the time course of cell attachment and spreading as a function of seeding density for three widespread and frequently used cell lines (MDCK strains I and II and Swiss 3T3-fibroblasts). Results were found to be in good agreement with the geometrical properties of the individual cell types. The shifts of the resonance frequency associated with confluent cell layers on top of the quartz resonators were found to be dependent on the cell species [MDCK-I: (320±20) Hz; MDCK-II: (530±25) Hz; 3T3: (240±15) Hz] reflecting their individual influence on the shear oscillation of the resonator. These findings are discussed with respect to the basic models of materials in contact with an oscillating quartz resonator. We furthermore showed by inhibition-assays using soluble RGD-related peptides, that only specific, integrin mediated cell adhesion is detected using this QCM approach, whereas the sole presence of the cellular body in close vicinity to the resonator surface is barely detectable.     

Do Svalbard reindeer regulate standing crop in the absence of predators?

The Svalbard reindeer is the only mammalian herbivore in Adventdalen (78°N), Svalbard, where it has no natural predators. To test if herbivores in the absence of predators regulate standing crop to a level independent of productivity, which is one of the predictions of the “exploitation ecosystems” model, herbivore exclosures were set up in 1992 in Salix heath, Luzula heath, Cassiope heath, and Alopecurus meadow in Adventdalen. Standing crop of vascular plants was harvested and measured inside and outside the exclosures in 1994, when the reindeer population was at peak density (ca 5.4 animals km⁻²), and in 1996, when the reindeer density was about 30% lower (ca 3.7 animals km⁻²). Standing dead material was reduced by grazing in the Luzula heath in 1994. However, we found no effect of grazing, year, or interactions between grazing and year on live standing crop. Also contrary to the predictions from the model, differences in standing crop between vegetation types were highly significant. Mean biomass of plant material was lowest in the Alopecurus meadow (36 g m⁻²), two fold higher in the Luzula heath, and about threefold higher in the Salix heath and Cassiope heath, indicating that reindeer do not regulate standing crop to the same level on a local scale. The predictive power of the “exploitation ecosystems” model is low due to lack of recognition of the importance of plant chemistry, plant compensation ability, variation in forage availability during the year, parasites functioning as predators, and adverse weather conditions, which may cause density-independent variations in fecundity and mortality of reindeer. Received: 28 December 1997 / Accepted: 6 April 1998     

Deep transformation models for functional outcome prediction after acute ischemic stroke

In many medical applications, interpretable models with high prediction performance are sought. Often, those models are required to handle semistructured data like tabular and image data. We show how to apply deep transformation models (DTMs) for distributional regression that fulfill these requirements. DTMs allow the data analyst to specify (deep) neural networks for different input modalities making them applicable to various research questions. Like statistical models, DTMs can provide interpretable effect estimates while achieving the state-of-the-art prediction performance of deep neural networks. In addition, the construction of ensembles of DTMs that retain model structure and interpretability allows quantifying epistemic and aleatoric uncertainty. In this study, we compare several DTMs, including baseline-adjusted models, trained on a semistructured data set of 407 stroke patients with the aim to predict ordinal functional outcome three months after stroke. We follow statistical principles of model-building to achieve an adequate trade-off between interpretability and flexibility while assessing the relative importance of the involved data modalities. We evaluate the models for an ordinal and dichotomized version of the outcome as used in clinical practice. We show that both tabular clinical and brain imaging data are useful for functional outcome prediction, whereas models based on tabular data only outperform those based on imaging data only. There is no substantial evidence for improved prediction when combining both data modalities. Overall, we highlight that DTMs provide a powerful, interpretable approach to analyzing semistructured data and that they have the potential to support clinical decision-making.     

Phage Types of Salmonella enterica ssp. enterica serovar Typhimurium Isolated from Production Animals and Humans i Denmark

S. Typhimurium is one of the 2 most common salmonella serotypes causing human salmonellosis in Denmark. In order to illustrate the significance of different production animals as a source of infection, 1461 isolates were characterized by phage typing. The isolates originated from human patients and from cattle, pigs and poultry. By phage typing the isolates could be separated in 35 different phage types. Five types (10, 12, 66, 110 and 135) predominated and comprised 78.8% of the isolates. In humans, 57.3% of the isolates were phage type 12. This phage type was also predominant in pig herds and, to a lesser degree, in cattle. Phage types 110, 120, 135 and 193 constituted 86.5% of the poultry isolates while these phage types only made up 12.9% of the human isolates. The investigation showed that pigs are probably a major source of S. Typhimurium infection in humans in Denmark today.