Multivariate meta-analysis of proteomics data from human prostate and colon tumours

Background  

There is a vast need to find clinically applicable protein biomarkers as support in cancer diagnosis and tumour classification. In proteomics research, a number of methods can be used to obtain systemic information on protein and pathway level on cells and tissues. One fundamental tool in analysing protein expression has been two-dimensional gel electrophoresis (2DE). Several cancer 2DE studies have reported partially redundant lists of differently expressed proteins. To be able to further extract valuable information from existing 2DE data, the power of a multivariate meta-analysis will be evaluated in this work.     

Facies analysis of a large-scale Jurassic shelf-lagoon: the Kamar-e-Mehdi Formation of east-central Iran

The Callovian–Lower Kimmeridgian Kamar-e-Mehdi Formation of the Tabas Block (east-central Iran) is an up to 1,350-m-thick, fine-grained, marly-calcareous unit containing a basal Echellon Limestone Member (up to 180 m thick) and a terminal Nar Limestone Member (up to 100 m thick). The formation was deposited in a relatively deep shelf-lagoon that was part of the large-scale carbonate system of the Esfandiar Subgroup, extending N–S for about 500 km along the strike with a width of up to 100 km. The lagoonal Kamar-e-Mehdi Formation shows sedimentation rates of 150 m/myr, twice as high as those of the shelf-edge carbonate barrier (Esfandiar Platform). The repetitive lithologies and uniform depositional environment suggest equilibrium conditions between sedimentation and subsidence, related to constant slow rotation of the Tabas fault-block around a horizontal axis, the platform sitting on the crest, and the lagoon occupying the dip-slope. Lagoonal sedimentation was dominated by suspended carbonate mud and peloids from the eastern Esfandiar Platform whereas the subordinate siliciclastic material was derived from the west (Yazd Block). The diverse macrobenthos (mainly bivalves) suggests fully marine conditions for the major part of the Kamar-e-Mehdi Formation. However, towards the upper part, biotic impoverishment and the deposition of skeletal-poor, evaporitic sediments indicate increasing restriction. The overlying Magu Gypsum Formation marks the end of an arid basin-fill cycle and possibly forms an effective seal for hydrocarbon reservoirs in that area. The Esfandiar Subgroup was a Neotethys-facing carbonate margin, forming part of a belt of carbonate systems tracking the margins of the Iran Plate during Callovian to Late Jurassic times.     

Leptotene/zygotene chromosome movement via the SUN/KASH protein bridge in Caenorhabditis elegans

The Caenorhabditis elegans inner nuclear envelope protein matefin/SUN-1 plays a conserved, pivotal role in the process of genome haploidization. CHK-2-dependent phosphorylation of SUN-1 regulates homologous chromosome pairing and interhomolog recombination in Caenorhabditis elegans. Using time-lapse microscopy, we characterized the movement of matefin/SUN-1::GFP aggregates (the equivalent of chromosomal attachment plaques) and showed that the dynamics of matefin/SUN-1 aggregates remained unchanged throughout leptonene/zygotene, despite the progression of pairing. Movement of SUN-1 aggregates correlated with chromatin polarization. We also analyzed the requirements for the formation of movement-competent matefin/SUN-1 aggregates in the context of chromosome structure and found that chromosome axes were required to produce wild-type numbers of attachment plaques. Abrogation of synapsis led to a deceleration of SUN-1 aggregate movement. Analysis of matefin/SUN-1 in a double-strand break deficient mutant revealed that repair intermediates influenced matefin/SUN-1 aggregate dynamics. Investigation of movement in meiotic regulator mutants substantiated that proper orchestration of the meiotic program and effective repair of DNA double-strand breaks were necessary for the wild-type behavior of matefin/SUN-1 aggregates.     

Pralidoxime in Acute Organophosphorus Insecticide Poisoning—A Randomised Controlled Trial

Background

Poisoning with organophosphorus (OP) insecticides is a major global public health problem, causing an estimated 200,000 deaths each year. Although the World Health Organization recommends use of pralidoxime, this antidote''s effectiveness remains unclear. We aimed to determine whether the addition of pralidoxime chloride to atropine and supportive care offers benefit.

Methods and Findings

We performed a double-blind randomised placebo-controlled trial of pralidoxime chloride (2 g loading dose over 20 min, followed by a constant infusion of 0.5 g/h for up to 7 d) versus saline in patients with organophosphorus insecticide self-poisoning. Mortality was the primary outcome; secondary outcomes included intubation, duration of intubation, and time to death. We measured baseline markers of exposure and pharmacodynamic markers of response to aid interpretation of clinical outcomes. Two hundred thirty-five patients were randomised to receive pralidoxime (121) or saline placebo (114). Pralidoxime produced substantial and moderate red cell acetylcholinesterase reactivation in patients poisoned by diethyl and dimethyl compounds, respectively. Mortality was nonsignificantly higher in patients receiving pralidoxime: 30/121 (24.8%) receiving pralidoxime died, compared with 18/114 (15.8%) receiving placebo (adjusted hazard ratio [HR] 1.69, 95% confidence interval [CI] 0.88–3.26, p = 0.12). Incorporating the baseline amount of acetylcholinesterase already aged and plasma OP concentration into the analysis increased the HR for patients receiving pralidoxime compared to placebo, further decreasing the likelihood that pralidoxime is beneficial. The need for intubation was similar in both groups (pralidoxime 26/121 [21.5%], placebo 24/114 [21.1%], adjusted HR 1.27 [95% CI 0.71–2.29]). To reduce confounding due to ingestion of different insecticides, we further analysed patients with confirmed chlorpyrifos or dimethoate poisoning alone, finding no evidence of benefit.

Conclusions

Despite clear reactivation of red cell acetylcholinesterase in diethyl organophosphorus pesticide poisoned patients, we found no evidence that this regimen improves survival or reduces need for intubation in patients with organophosphorus insecticide poisoning. The reason for this failure to benefit patients was not apparent. Further studies of different dose regimens or different oximes are required.

Trial Registration

Controlled-trials.com ISRCTN55264358 Please see later in the article for Editors'' Summary     

Endothelial Dysfunction and Brachial Intima-Media Thickness: Long Term Cardiovascular Risk with Claudication Related to Peripheral Arterial Disease: A Prospective Analysis

Objective

Endothelial dysfunction plays a key role in the development, progression, and clinical manifestation of atherosclerosis, and in symptomatic peripheral arterial disease, endothelial dysfunction and enlarged intima-media thickness might be associated with increased cardiovascular risk. Flow-mediated dilatation and serologic parameters are used to evaluate individual endothelial function. Brachial intima-media thickness, a less recognized parameter of cardiovascular risk, is independently associated with coronary artery disease. The aim of this study was to evaluate the prognostic value of ultrasound and serologic parameters of endothelial function in relation to cardiovascular mortality in peripheral arterial disease.

Design

monocentric, prospective cohort study.

Methods

Flow mediated dilatation and brachial intima-media thickness were assessed in 184 (124 male) patients with peripheral arterial disease (Rutherford stages 2–3). Serologic parameters of endothelial function included asymmetric dimethylarginine (ADMA), symmetric dimethylarginine (SDMA), and L-homoarginine. Cardiovascular events were recorded during a follow-up of 99.1±11.1 months. Subjects who died of noncardiovascular causes were excluded from further analysis.

Results

Eighty-two patients (44.6%) died during follow-up after a mean duration of 49.7±28.3 months. There were 49 cardiovascular deaths (59.8%) and 33 other deaths (40.2%). Flow mediated dilatation was associated with cardiovascular death [1.17% (0.0, 4.3) vs. 4.1% (1.2, 6.4), p<0.001]. Intima-media thickness was greater in patients who succumbed to cardiovascular disease [0.37 mm (0.30, 0.41)] than in survivors [0.21 mm (0.15, 0.38), p<0.001]. Brachial intima-media thickness above 0.345 mm was most predictive of cardiovascular death, with sensitivity and specificity values of 0.714 and 0.657, respectively (p<0.001). Furthermore, ADMA levels above 0.745 µmol/l and SDMA levels above 0.825 µmol/l were significantly associated with cardiovascular death (p<0.001 and 0.030).

Conclusion

In symptomatic peripheral arterial disease, decreased flow mediated dilatation, enlarged intima-media thickness, and elevated levels of ADMA and SDMA were associated with increased cardiovascular risk.     

Unifying Charge Generation,Recombination, and Extraction in Low‐Offset Non‐Fullerene Acceptor Organic Solar Cells

Even though significant breakthroughs with over 18% power conversion efficiencies (PCEs) in polymer:non‐fullerene acceptor (NFA) bulk heterojunction organic solar cells (OSCs) have been achieved, not many studies have focused on acquiring a comprehensive understanding of the underlying mechanisms governing these systems. This is because it can be challenging to delineate device photophysics in polymer:NFA blends comprehensively, and even more complicated to trace the origins of the differences in device photophysics to the subtle differences in energetics and morphology. Here, a systematic study of a series of polymer:NFA blends is conducted to unify and correlate the cumulative effects of i) voltage losses, ii) charge generation efficiencies, iii) non‐geminate recombination and extraction dynamics, and iv) nuanced morphological differences with device performances. Most importantly, a deconvolution of the major loss processes in polymer:NFA blends and their connections to the complex BHJ morphology and energetics are established. An extension to advanced morphological techniques, such as solid‐state NMR (for atomic level insights on the local ordering and donor:acceptor π? π interactions) and resonant soft X‐ray scattering (for donor and acceptor interfacial area and domain spacings), provide detailed insights on how efficient charge generation, transport, and extraction processes can outweigh increased voltage losses to yield high PCEs.     

Animal movement in the absence of predation: environmental drivers of movement strategies in a partial migration system

Animal movement strategies including migration, dispersal, nomadism, and residency are shaped by broad‐scale spatial‐temporal structuring of the environment, including factors such as the degrees of spatial variation, seasonality and inter‐annual predictability. Animal movement strategies, in turn, interact with the characteristics of individuals and the local distribution of resources to determine local patterns of resource selection with complex and poorly understood implications for animal fitness. Here we present a multi‐scale investigation of animal movement strategies and resource selection. We consider the degree to which spatial variation, seasonality, and inter‐annual predictability in resources drive migration patterns among different taxa and how movement strategies in turn shape local resource selection patterns. We focus on adult Galapagos giant tortoises Chelonoidis spp. as a model system since they display many movement strategies and evolved in the absence of predators of adults. Specifically, our analysis is based on 63 individuals among four taxa tracked on three islands over six years and almost 10⁶ tortoise re‐locations. Tortoises displayed a continuum of movement strategies from migration to sedentarism that were linked to the spatio‐temporal scale and predictability of resource distributions. Movement strategies shaped patterns of resource selection. Specifically, migratory individuals displayed stronger selection toward areas where resources were more predictable among years than did non‐migratory individuals, which indicates a selective advantage for migrants in seasonally structured, more predictable environments. Our analytical framework combines large‐scale predictions for movement strategies, based on environmental structuring, with finer‐scale analysis of space‐use. Integrating different organizational levels of analysis provides a deeper understanding of the eco‐evolutionary dynamics at play in the emergence and maintenance of migration and the critical role of resource predictability. Our results highlight that assessing the potential benefits of differential behavioral responses first requires an understanding of the interactions among movement strategies, resource selection and individual characteristics.     

The carotenoids of Flavobacterium strain R1560

The main carotenoid of Flavobacterium strain R1560 has been identified as (3R,3R)-zeaxanthin. Also present were small amounts of 15-cis-phytoene, phytofluene, -carotene (7,8,7,8-tetrahydro-, -carotene plus 7,8,11,12-tetrahydro-, -carotene), neurosporene, lycopene, -zeacarotene, -carotene, -carotene, -cryptoxanthin, rubixanthin, 3-hydroxy--zeacarotene and several apo-carotenals. Zeaxanthin production was inhibited by nicotine (10 mM), and lycopene and rubixanthin accumulated. The biosynthesis of zeaxanthin is discussed in terms of pathways and also of half-molecule reaction sequences. The presence of zeaxanthin may be a characteristic of a group of Flavobacterium species, and may thus be useful in the taxonomic classification of these organisms.     

Endogene Synthese kurzlebiger Messenger-RNS in der Oocyte vonDysdercus intermedius Dist. nach Abschluß der Vitellogenese

Zusammenfassung In den Oocyten des telotroph-meroistischen Ovars vonDysdercus intermedius Dist. findet während der Endphase der Oogenese, 4–14 h vor der Eiablage, eine Synthese von nichtribosomaler RNS statt. Eine in vivo-Markierung dieser RNS läßt sich erreichen, wenn radioaktive RNS-Vorstufen einem Nucleotidpool zugeführt werden, der im Ooplasma vor der Chorionbildung angelegt wird.Diese vor der Eiablage gebildete RNS zeichnet sich durch einen hohen Turnover aus. Sie erscheint zunächst in Form einer hochmolekularen Vorstufe und wird im Verlauf weniger Stunden in kleinere, nichtribosomale Moleküle mit S-Werten zwischen 30 und 5 umgewandelt. Im frisch abgelegten Ei fehlen RNS-Spezies, die dieser endogenen Oocytensynthese entstammen; es sind nur noch ihre Degradationsprodukte, die sich innerhalb der Nucleotidfraktion ansammeln, nachweisbar. Die endogen synthetisierte RNS wird demnach im Gegensatz zu der in den Nährzellen synthetisierten und im Ei in stabiler Form gespeicherten RNS nicht für einen Bedarf während der Embryogenese konserviert.Die endogen synthetisierte RNS zeichnet sich durch einen hohen Poly (A)-Gehalt aus; 57% hybridisieren mit an Glasfaserfiltern immobilisiertem Poly(U). Wenige Stunden vor der Eiablage findet man kurzlebige oocytäre RNS-Moleküle an Polysomen assoziiert. Die Inkubation dieser Polysomen in einem in vitro-Proteinsynthese-System liefert Polypeptide, deren Auftrennung am SDS-Polyacrylamid-Gel ein charakteristisches Bandenspektrum ergibt. Die Molekulargewichte der 4 Hauptbanden liegen bei 65000, 48000, 44000, und 40000. Keines dieser Proteine ist mit einem Chorionprotein identisch.Die Kurzlebigkeit, der relativ hohe Poly (A)-Gehalt sowie die Fähigkeit, die Proteinsynthese sowohl in vivo als auch in vitro zu aktivieren, spricht dafür, daß die spät-oocytär gebildete heterogene Population von RNS-Molekülen mRNS-Komponenten enthält.Bei Frl. Heidrun Greipel bedanken wir uns für die ausgezeichnète Assistenz.