In vivo crystal formation in Escherichia coli of an over-expressed soluble form of penicillin-binding protein 5

Accumulation of either native membrane-bound or soluble variants of PBP5 over-expressed in the cytoplasm was investigated by electron microscopy of ultra-thin sections. One of the soluble forms of PBP5 (PBP5s353) formed well-ordered crystals inside the cells. Cells sectioned perpendicular to their long axis showed a diamond-shaped crystal whereas cells cut parallel to their long axis contained a long, narrow crystal. In both sectioning directions an ordered ultrastructure was visible as shown by optical diffraction. Computer processing was used to enhance the crystal images. From this the unit cell parameters were calculated as a = 7.6 nm, b = 4 nm, c = 4.2 nm, gamma = 75 degrees. The calculated unit-cell volume of 120 nm3 is large enough to contain one protein molecule.     

Mining oomycete proteomes for metalloproteases leads to identification of candidate virulence factors in Phytophthora infestans

Pathogens deploy a wide range of pathogenicity factors, including a plethora of proteases, to modify host tissue or manipulate host defences. Metalloproteases (MPs) have been implicated in virulence in several animal and plant pathogens. Here we investigated the repertoire of MPs in 46 stramenopile species including 37 oomycetes, 5 diatoms, and 4 brown algae. Screening their complete proteomes using hidden Markov models (HMMs) trained for MP detection resulted in over 4,000 MPs, with most species having between 65 and 100 putative MPs. Classification in clans and families according to the MEROPS database showed a highly diverse MP repertoire in each species. Analyses of domain composition, orthologous groups, distribution, and abundance within the stramenopile lineage revealed a few oomycete-specific MPs and MPs potentially related to lifestyle. In-depth analyses of MPs in the plant pathogen Phytophthora infestans revealed 91 MPs, divided over 21 protein families, including 25 MPs with a predicted signal peptide or signal anchor. Expression profiling showed different patterns of MP gene expression during pre-infection and infection stages. When expressed in leaves of Nicotiana benthamiana, 12 MPs changed the sizes of lesions caused by inoculation with P. infestans; with 9 MPs the lesions were larger, suggesting a positive effect on the virulence of P. infestans, while 3 MPs had a negative effect, resulting in smaller lesions. To the best of our knowledge, this is the first systematic inventory of MPs in oomycetes and the first study pinpointing MPs as potential pathogenicity factors in Phytophthora.     

A Neurocomputational Model of the Mismatch Negativity

The mismatch negativity (MMN) is an event related potential evoked by violations of regularity. Here, we present a model of the underlying neuronal dynamics based upon the idea that auditory cortex continuously updates a generative model to predict its sensory inputs. The MMN is then modelled as the superposition of the electric fields evoked by neuronal activity reporting prediction errors. The process by which auditory cortex generates predictions and resolves prediction errors was simulated using generalised (Bayesian) filtering – a biologically plausible scheme for probabilistic inference on the hidden states of hierarchical dynamical models. The resulting scheme generates realistic MMN waveforms, explains the qualitative effects of deviant probability and magnitude on the MMN – in terms of latency and amplitude – and makes quantitative predictions about the interactions between deviant probability and magnitude. This work advances a formal understanding of the MMN and – more generally – illustrates the potential for developing computationally informed dynamic causal models of empirical electromagnetic responses.     

Quelques remarques sur l'holisme dans la pensée grecque

Summary The conception of the world with Greek thinkers generally differs from contemporary thought in the idea of the limitation of the world whose essence manifests itself to speculative thinking. The cosmology which culminates inPlato's Timaios attributes to the whole of being the properties of finiteness, uniqueness, life and perfection.Plato's holism subsumes inanimate and living nature under the idea of cosmic life, the parts of which are constituted by life-phenomena given in experience. His world-conception, constructed from within and intuitively, which ranges phenomena in descending order, is opposed to the atomism ofDemocritos which reduces the higher structures to the one equal material of all things. This opposition manifests itself in all essential points: toDemocritos there are worlds in infinite number, only accumulations of atoms are real, uniqueness and perfection are lacking as well as the idea of Life as a central reality.Modern research foregoes the attempt to determine the whole speculatively, but holistic and atomistic ways of thinking, after having been dogmatically applied by the Greeks, continue to exist as opposed types of mental attitude. Contemporary holism may be empirical and limited in application, but it is directed by the same intuition of life articulating itself organically as wasPlato's. It would be incorrect, however, to characterize holism as synthetical, since all synthetics is based upon analysis. The bounds of synthesis are never fixed ones, nor does it ever determine essence. Holism's way of subsuming single life-phenomena under more comprehensive wholes is an intuitional one, the connections which it creates between phenomena are not external ones, but apprehended intuitively in analogy to inner experience.—In distinction to atomism, which only admits as real atoms and their mutual relations, holism poses groups of unities, classified in grades, the higher of which dominate the lower, without debasing them to elements. As metaphysics is concerned to discover a connection between Nature and human life, it must be highly interested in the empirical demonstration, such as holism offers, of connections of life, surpassing individual being.

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Zusammenfassung Die griechische Weltauffassung unterscheidet sich van der modernen durch den Gedanken der Begrenztheit des Weltalls, das sich dem spekulativen Blick seinem Wesen nach erschliesst. Die inPlaton's Timaios gipfelnde Kosmologie bestimmt das Weltall nach den Wesensgesichtspunkten der Endlichkeit, der Einzigkeit, der Lebendigkeit und der Vollkommenheit.Platon's Holismus bezieht die leblose und die lebende Natur unter die Idee des Lebens des Kosmos, dessen Teile die in der Erfahrung gegebenen Lebenserscheinungen sind. Sein von innen her und intuitiv aufgebautes Weltbild, das die Erscheinungen von oben herab hierarchisch ordnet, tritt dem AtomismusDemokrits gegenüber, der in umgekehrtem Verfahren die höheren Strukturen auf den einen Baustoff aller Dinge reduziert. Der Gegensatz zum Holismus offenbart sich in allen Bestimmungen: fürDemokrit sind der Kosmoi unbegrenzt viele, es gibt nur Ansammlungen von Atomen, es fehlen Einzigkeit und Vollkommenheit, sowie ein Begriff des Lebens als des zentralen Geschehens.Die neuzeitliche Forschung verzichtet auf die spekulativen Bestimmungen des Ganzen, aber der bei den Griechen dogmatische Gegensatz holistischer und atomistischer Betrachtungsweise lebt fort als Gegensatz geistiger Einstellung. Der neuzeitliche Holismus ist ein empirischer, beschränkter, aber bei ihm liegt dieselbe Intuition des sich organisch gestaltenden Gesamtlebens zu Grunde wei beiPlaton. Nur wäre es, unrichtig, diesen Holismus als synthetisch zu bezeichnen. Synthetisches Denken erhebt sich immer auf analytischem Boden. Jede Synthese hat eine offene Grenze. Die Art aber, wie der Holismus die vereinzelten Lebenserscheinungen auf umfassendere Ganzheiten bezieht, ist eine intuitive. Das Band der Erscheinungen wird nicht durch äusseres Beziehen gestiftet, sondern geschaut nach Analogie einer inneren Erfahrung.Im Gegensatz zum Atomismus, der als real nur die Atome und deren Verhältnisse gelten lässt, erkennt der Holismus stufenartig aufgebaute Einheitsarten an, in denen die höheren die niedrigeren beherrschen, ohne sie zu Elementen herabzudrücken. Die Metaphysik, auf der Suche nach dem Zusammenhang zwischen dem Menschenleben und der Natur ist an der empirischen Aufweisung das Einzelne übersteigender Lebensverbände wie sie der Holismus zu Tage fordert aufs Höchste interessiert.

     

Tracking niche variation over millennial timescales in sympatric killer whale lineages

Niche variation owing to individual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic ratios were measured from tissue samples of sympatric killer whale Orcinus orca lineages from the North Sea, spanning over 10 000 years. Isotopic ratios spanned a range similar to the difference in isotopic values of two known prey items, herring Clupea harengus and harbour seal Phoca vitulina. Two proxies of the stage of speciation, lineage sorting of mitogenomes and genotypic clustering, were both weak to intermediate indicating that speciation has made little progress. Thus, our study confirms that even with the necessary ecological conditions, i.e. among-individual variation in ecology, it is difficult for sympatric speciation to progress in the face of gene flow. In contrast to some theoretical models, our empirical results suggest that sympatric speciation driven by among-individual differences in ecological niche is a slow process and may not reach completion. We argue that sympatric speciation is constrained in this system owing to the plastic nature of the behavioural traits under selection when hunting either mammals or fish.     

The Outer Membrane TolC-like Channel HgdD Is Part of Tripartite Resistance-Nodulation-Cell Division (RND) Efflux Systems Conferring Multiple-drug Resistance in the Cyanobacterium Anabaena sp. PCC7120

The TolC-like protein HgdD of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120 is part of multiple three-component “AB-D” systems spanning the inner and outer membranes and is involved in secretion of various compounds, including lipids, metabolites, antibiotics, and proteins. Several components of HgdD-dependent tripartite transport systems have been identified, but the diversity of inner membrane energizing systems is still unknown. Here we identified six putative resistance-nodulation-cell division (RND) type factors. Four of them are expressed during late exponential and stationary growth phase under normal growth conditions, whereas the other two are induced upon incubation with erythromycin or ethidium bromide. The constitutively expressed RND component Alr4267 has an atypical predicted topology, and a mutant strain (I-alr4267) shows a reduction in the content of monogalactosyldiacylglycerol as well as an altered filament shape. An insertion mutant of the ethidium bromide-induced all7631 did not show any significant phenotypic alteration under the conditions tested. Mutants of the constitutively expressed all3143 and alr1656 exhibited a Fox⁻ phenotype. The phenotype of the insertion mutant I-all3143 parallels that of the I-hgdD mutant with respect to antibiotic sensitivity, lipid profile, and ethidium efflux. In addition, expression of the RND genes all3143 and all3144 partially complements the capability of Escherichia coli ΔacrAB to transport ethidium. We postulate that the RND transporter All3143 and the predicted membrane fusion protein All3144, as homologs of E. coli AcrB and AcrA, respectively, are major players for antibiotic resistance in Anabaena sp. PCC 7120.     

A change in the pattern in circadian running‐wheel activity after lesions of the intergeniculate leaflet and ventral lateral geniculate nucleus in the Syrian hamster

Abstract

The suprachiasmatic nuclei (SCN) contain the endogenous mammalian circadian pacemaker, which generates the circadian rhythm in locomotor activity. In Syrian hamsters with free‐running rhythms, the onset of running‐wheel activity is very precise and predictable while the end (offset) is more variable. From the thalamic intergeniculate leaflet (IGL) and the ventral lateral geniculate nucleus (vLGN) a projection to the SCN originates. Animals with a lesion aimed at the IGL/vLGN and sham‐and unoperated controls were kept in continuous darkness. With linear regression, lines were fitted through 10 successive onsets and offsets of activity and the mean deviation of the onsets and offsets from the fitted lines was determined. Animals with a complete or partial lesion of the IGL/vLGN had a smaller mean deviation of the circadian activity offset from the fitted regression line (0.313 h) compared with the grouped control animals (0.678 h). To test the difference statistically, we compared the sum of the square residuals of the circadian offsets between the groups. This difference was highly significant (F(69,64)=4.16, p<0.0001), which indicates that animals with a lesion of the IGL/ vLGN have a less variable circadian offset of running‐wheel activity. No differences were observed in the variability in the circadian onset of locomotor activity between experimental and control animals. It is concluded that the IGL/vLGN influence the variability of the offset of the circadian running‐wheel activity.     

Embryonic Cardiomyocyte,but Not Autologous Stem Cell Transplantation,Restricts Infarct Expansion,Enhances Ventricular Function,and Improves Long-Term Survival

Aims

Controversy exists in regard to the beneficial effects of transplanting cardiac or somatic progenitor cells upon myocardial injury. We have therefore investigated the functional short- and long-term consequences after intramyocardial transplantation of these cell types in a murine lesion model.

Methods and Results

Myocardial infarction (MI) was induced in mice (n = 75), followed by the intramyocardial injection of 1−2×10⁵ luciferase- and GFP-expressing embryonic cardiomyocytes (eCMs), skeletal myoblasts (SMs), mesenchymal stem cells (MSCs) or medium into the infarct. Non-treated healthy mice (n = 6) served as controls. Bioluminescence and fluorescence imaging confirmed the engraftment and survival of the cells up to seven weeks postoperatively. After two weeks MRI was performed, which showed that infarct volume was significantly decreased by eCMs only (14.8±2.2% MI+eCM vs. 26.7±1.6% MI). Left ventricular dilation was significantly decreased by transplantation of any cell type, but most efficiently by eCMs. Moreover, eCM treatment increased the ejection fraction and cardiac output significantly to 33.4±2.2% and 22.3±1.2 ml/min. In addition, this cell type exclusively and significantly increased the end-systolic wall thickness in the infarct center and borders and raised the wall thickening in the infarct borders. Repetitive echocardiography examinations at later time points confirmed that these beneficial effects were accompanied by better survival rates.

Conclusion

Cellular cardiomyoplasty employing contractile and electrically coupling embryonic cardiomyocytes (eCMs) into ischemic myocardium provoked significantly smaller infarcts with less adverse remodeling and improved cardiac function and long-term survival compared to transplantation of somatic cells (SMs and MSCs), thereby proving that a cardiomyocyte phenotype is important to restore myocardial function.     

Physiological Response of Adipocytes to Weight Loss and Maintenance

Background

Metabolic processes in adipose tissue are dysregulated in obese subjects and, in response to weight loss, either normalize or change in favor of weight regain.

Objective

To determine changes in adipocyte glucose and fatty acid metabolism in relation to changes in adipocyte size during weight loss and maintenance.

Methods

Twenty-eight healthy subjects (12 males), age 20–50 y, and BMI 28–35 kg/m², followed a very low energy diet for 2 months, followed by a 10-month period of weight maintenance. Body weight, body composition (deuterium dilution and BodPod), protein levels (Western blot) and adipocyte size were assessed prior to and after weight loss and after the 10-month follow-up.

Results

A 10% weight loss resulted in a 16% decrease in adipocyte size. A marker for glycolysis decreased (AldoC) during weight loss in association with adipocyte shrinking, and remained decreased during follow-up in association with weight maintenance. A marker for fatty acid transport increased (FABP4) during weight loss and remained increased during follow-up. Markers for mitochondrial beta-oxidation (HADHsc) and lipolysis (ATGL) were only increased after the 10-month follow-up. During weight loss HADHsc and ATGL were coordinately regulated, which became weaker during follow-up due to adipocyte size-related changes in HADHsc expression. AldoC was the major denominator of adipocyte size and body weight, whereas changes in ATGL during weight loss contributed to body weight during follow-up. Upregulation of ATGL and HADHsc occured in the absence of a negative energy balance and was triggered by adipocyte shrinkage or indicated preadipocyte differentiation.

Conclusion

Markers for adipocyte glucose and fatty acid metabolism are changed in response to weight loss in line with normalization from a dysregulated obese status to an improved metabolic status.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01015508","term_id":"NCT01015508"}}NCT01015508