Consistent probabilistic outputs for protein function prediction

In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one another; for example, the predictor may assign a specific GO term to a given protein ('purine nucleotide binding') but not assign the parent term ('nucleotide binding'). Such predictions are difficult to interpret. In this work, we focus on methods for calibrating and combining independent predictions to obtain a set of probabilistic predictions that are consistent with the topology of the ontology. We call this procedure 'reconciliation'. We begin with a baseline method for predicting GO terms from a collection of data types using an ensemble of discriminative classifiers. We apply the method to a previously described benchmark data set, and we demonstrate that the resulting predictions are frequently inconsistent with the topology of the GO. We then consider 11 distinct reconciliation methods: three heuristic methods; four variants of a Bayesian network; an extension of logistic regression to the structured case; and three novel projection methods - isotonic regression and two variants of a Kullback-Leibler projection method. We evaluate each method in three different modes - per term, per protein and joint - corresponding to three types of prediction tasks. Although the principal goal of reconciliation is interpretability, it is important to assess whether interpretability comes at a cost in terms of precision and recall. Indeed, we find that many apparently reasonable reconciliation methods yield reconciled probabilities with significantly lower precision than the original, unreconciled estimates. On the other hand, we find that isotonic regression usually performs better than the underlying, unreconciled method, and almost never performs worse; isotonic regression appears to be able to use the constraints from the GO network to its advantage. An exception to this rule is the high precision regime for joint evaluation, where Kullback-Leibler projection yields the best performance.     

Replication blocking lesions present a unique substrate for homologous recombination

Homologous recombination (HR) plays a critical role in the restart of blocked replication forks, but how this is achieved remains poorly understood. We show that mutants in the single Rad51 paralog in Caenorhabditis elegans, rfs-1, permit discrimination between HR substrates generated at DNA double-strand breaks (DSBs), or following replication fork collapse from HR substrates assembled at replication fork barriers (RFBs). Unexpectedly, RFS-1 is dispensable for RAD-51 recruitment to meiotic and ionizing radiation (IR)-induced DSBs and following replication fork collapse, yet, is essential for RAD-51 recruitment to RFBs formed by DNA crosslinking agents and other replication blocking lesions. Deletion of rfs-1 also suppresses the accumulation of toxic HR intermediates in him-6; top-3 mutants and accelerates deletion formation at presumed endogenous RFBs formed by poly G/C tracts in the absence of DOG-1. These data suggest that RFS-1 is not a general mediator of HR-dependent DSB repair, but acts specifically to promote HR at RFBs. HR substrates generated at conventional DSBs or following replication fork collapse are therefore intrinsically different from those produced during normal repair of blocked replication forks.     

Trophic cul-de-sac, Pyrazus ebeninus, limits trophic transfer through an estuarine detritus-based food web

The importance to food‐webs of trophic cul‐de‐sacs, species that channel energy flow away from higher trophic levels, is seldom considered outside of the pelagic systems in which they were first identified. On intertidal mudflats, inputs of detritus from saltmarshes, macroalgae or microphytobenthos are generally regarded as a major structuring force underpinning food‐webs and there has been no consideration of trophic cul‐de‐sacs to date. A fully orthogonal three‐factor experiment manipulating the density of the abundant gastropod, Pyrazus ebeninus, detritus and macrobenthic predators on a Sydney mudflat revealed large deleterious effects of the gastropod, irrespective of detrital loading or the presence of predators. Two months after experimental manipulation, the standing‐stock of microphytobenthos in plots with high (44 per m²) densities of P. ebeninus was 20% less than in plots with low (4 per m²) densities. Increasing densities of P. ebeninus from low to high halved the abundance of macroinvertebrates and the average number of species. In contrast, the addition of detritus had differing effects on microphytobenthos (positively affected) and macroinvertebrates (negatively affected). Over the two‐months of our experiment, no predatory mortality of P. ebeninus was observed and high densities of P. ebeninus decreased impacts of predators on macroinvertebrate abundances. Given that the dynamics of southeast Australian mudflats are driven more by disturbance than seasonality in predators and their interactions with prey, it is likely that Pyrazus would be similarly resistant to predation and have negative effects on benthic assemblages at other times of the year, outside of our study period. Thus, in reducing microphytobenthos and the abundance and species richness of macrofauna, high abundances of the detritivore P. ebeninus may severely limit the flow of energy up the food chain to commercially‐important species. This study therefore suggests that trophic cul‐de‐sacs are not limited to the eutrophied pelagic systems in which they were first identified, but may exist in other systems as well.     

Cnn dynamics drive centrosome size asymmetry to ensure daughter centriole retention in Drosophila neuroblasts

Centrosomes comprise a pair of centrioles surrounded by an amorphous network of pericentriolar material (PCM). In certain stem cells, the two centrosomes differ in size, and this appears to be important for asymmetric cell division [1, 2]. In some cases, centrosome asymmetry is linked to centriole age because the older, mother centriole always organizes more PCM than the daughter centriole, thus ensuring that the mother centriole is always retained in the stem cell after cell division [3]. This has raised the possibility that an "immortal" mother centriole may help maintain stem cell fate [4, 5]. It is unclear, however, how centrosome size asymmetry is generated in stem cells. Here we provide compelling evidence that centrosome size asymmetry in Drosophila neuroblasts is generated by the differential regulation of Cnn incorporation into the PCM at mother and daughter centrioles. Shortly after centriole separation, mother and daughter centrioles organize similar amounts of PCM, but Cnn incorporation is then rapidly downregulated at the mother centriole, while it is maintained at the daughter centriole. This ensures that the daughter centriole maintains its PCM and so its position at the apical cortex. Thus, the?daughter centriole, rather than an "immortal" mother centriole, is ultimately retained in these stem cells.     

Efficient immunization and cross-priming by vaccine adjuvants containing TLR3 or TLR9 agonists complexed to cationic liposomes

Complexing TLR9 agonists such as plasmid DNA to cationic liposomes markedly potentiates their ability to activate innate immunity. We therefore reasoned that liposomes complexed with DNA or other TLR agonists could be used as effective vaccine adjuvants. To test this hypothesis, the vaccine adjuvant effects of liposomes complexed to TLR agonists were assessed in mice. We found that liposomes complexed to nucleic acids (liposome-Ag-nucleic acid complexes; LANAC) were particularly effective adjuvants for eliciting CD4(+) and CD8(+) T cell responses against peptide and protein Ags. Notably, LANAC containing TLR3 or TLR9 agonists effectively cross-primed CD8(+) T cell responses against even low doses of protein Ags, and this effect was independent of CD4(+) T cell help. Ag-specific CD8(+) T cells elicited by LANAC adjuvants were functionally active and persisted for long periods of time in tissues. In a therapeutic tumor vaccine model, immunization with the melanoma peptide trp2 and LANAC adjuvant controlled the growth of established B16 melanoma tumors. In a prophylactic vaccine model, immunization with the Mycobacterium tuberculosis protein ESAT-6 with LANAC adjuvant elicited significant protective immunity against aerosol challenge with virulent M. tuberculosis. These results suggest that certain TLR agonists can be combined with cationic liposomes to produce uniquely effective vaccine adjuvants capable of eliciting strong T cell responses against protein and peptide Ags.     

The effect of oral glucose loads on tissue metabolism during angiotensin II receptor and beta-receptor blockade in obese hypertensive subjects.

AT1 receptor blockers and ACE inhibitors decrease the risk for new onset diabetes mellitus. The phenomenon could be related to a direct angiotensin II effect on tissue metabolism. To address the issue, we recruited eighteen obese hypertensive patients. Patients were randomized to double-blind treatment with either valsartan (n = 8) or atenolol (n = 10) for thirteen weeks. They underwent an oral glucose tolerance test before and during active treatment, while metabolism was monitored through subcutaneous and intramuscular microdialysis and indirect calorimetry. After glucose ingestion, venous glucose and insulin concentrations increased rapidly while systemic free fatty acid concentrations were suppressed. Dialysate glucose and lactate concentrations increased briskly in adipose tissue and in skeletal muscle. Dialysate glycerol decreased profoundly in both tissues. Respiratory quotient increased markedly after glucose ingestion. These responses were identical at baseline and during active treatment either drug. We conclude that AT1 receptor blockade in obese hypertensive patients has no effect on interstitial glucose supply, lipolysis, and substrate oxidation. One possible explanation is that angiotensin II levels in obese hypertensives are not sufficient to elicit the metabolic changes that have been observed after direct angiotensin II application. The exact mechanism by which inhibition of the renin-angiotensin-aldosterone system decreases the diabetes risk remains unresolved and requires further study.     

Organization of Methanobacterium thermoautotrophicum bacteriophage psi M1 DNA

Summary M1 is a virulent bacteriophage of Methanobacterium thermoautotrophicum strain Marburg. Restriction enzyme analysis of the linear, 30.4 kb phage DNA led to a circular map of the 27.1 kb M1 genome. M1 is thus circularly permuted and exhibits terminal redundancy of approximately 3 kb. Packaging of M1 DNA from a concatemeric precursor initiates at the pac site which was identified at coordinate 4.6 kb on the circular genome map. It proceeds clockwise for at least five packaging rounds. Headful packaging was also shown for M2, a phage variant with a 0.7 kb deletion at coordinate 23.25 on the map.     

Autophagy and mitochondrial alterations in human retinal pigment epithelial cells induced by ethanol: implications of 4-hydroxy-nonenal

Retinal pigment epithelium has a crucial role in the physiology and pathophysiology of the retina due to its location and metabolism. Oxidative damage has been demonstrated as a pathogenic mechanism in several retinal diseases, and reactive oxygen species are certainly important by-products of ethanol (EtOH) metabolism. Autophagy has been shown to exert a protective effect in different cellular and animal models. Thus, in our model, EtOH treatment increases autophagy flux, in a concentration-dependent manner. Mitochondrial morphology seems to be clearly altered under EtOH exposure, leading to an apparent increase in mitochondrial fission. An increase in 2′,7′-dichlorofluorescein fluorescence and accumulation of lipid peroxidation products, such as 4-hydroxy-nonenal (4-HNE), among others were confirmed. The characterization of these structures confirmed their nature as aggresomes. Hence, autophagy seems to have a cytoprotective role in ARPE-19 cells under EtOH damage, by degrading fragmented mitochondria and 4-HNE aggresomes. Herein, we describe the central implication of autophagy in human retinal pigment epithelial cells upon oxidative stress induced by EtOH, with possible implications for other conditions and diseases.Retinal pigment epithelium (RPE) is a single neuroectodermal layer placed in the outermost part of the eye cup faced to photoreceptors.^{1, 2} Owing to its anatomical location and function, RPE is continuously exposed to potential cell damage caused by oxidative stress, specifically due to oxygen and nitrogen reactive species.³ This is probably one of the reasons why these cells are more resistant to oxidative stress.⁴ Oxidative stress is present as part of the pathophysiology in several retinal degenerations associated with blindness, for example, age-related macular degeneration,³ where RPE is considered a key factor for its development.⁵ Studies with the human-derived cell line ARPE-19 have proven to be very useful in the elucidation of the role of these cells in disease.Autophagy is a catabolic process aimed to degrade damaged organelles, proteins and cellular debris by engulfing them into a double membrane vesicle called the autophagosome and eliminating them by posterior fusion with the lysosome. Activation of macroautophagy, a form of autophagy, has been recently confirmed to be a primary response of ARPE-19 cells to stress.⁶ Furthermore, the two major functions of RPE, phagocytosis of the photoreceptor outer segments and visual cycle performance, have been linked to a noncanonical form of autophagy that is known as LC3 (microtubule-associated protein 1A/1B-light chain 3)-associated phagocytosis and is supposed to contribute to the normal supply of vitamin A and therefore to normal vision.^{7, 8}Despite its negative effects on health, ethanol (EtOH) is consumed daily worldwide, standing as one of the top public health challenges. EtOH induces morphological and physiological changes in the nervous tissue, and most of these changes may be attributed to reactive oxygen species (ROS), as they can be normalized or prevented by antioxidant treatments.^{9, 10, 11, 12, 13} Autophagy has been identified as cytoprotector in nervous and liver cells under EtOH-induced toxicity,^{14, 15} where it seems to degrade damaged organelles, including mitochondria. Recent findings support the idea that there is an increased mitochondrial stress and dysfunction in the RPE cells in AMD patients.^{16, 17} Oxidative-damaged mitochondria, a main source of ROS, seem to be removed by autophagy (known as mitophagy), in order to guarantee cell survival.¹⁸ As a matter of fact, deregulation of mitophagy has been implicated in several neurodegenerative diseases, such as Parkinson''s disease (PD), Alzheimer''s disease (AD) and Huntington''s disease (HD).Peroxidation of polyunsaturated fatty acids is intensified in cells subjected to oxidative stress, and results in the generation of various bioactive compounds, among others 4-hydroxyalkenals (HAE). ROS-induced lipid peroxidation and the resulting HAE markedly contribute to the development and progression of different diseases.¹⁹ Specifically, 4-hydroxy-nonenal (4-HNE), a major α,β-unsaturated aldehyde product of n-6 fatty acid oxidation, has been shown to be involved in a great number of maladies.²⁰ It has been reported that 4-HNE induces apoptosis in ARPE-19 cells²¹ and its ability to form protein adducts, thus it seems to be a key factor in aggresome formation. Aggresome is a term referred to cytoplasmic perinuclear inclusion bodies formed by aggregated proteins.²² Indeed, the presence of aggresomes is a pathological hallmark of most neurodegenerative diseases, and 4-HNE seems to be involved in their formation in AD,²³ PD,²⁴ HD²⁵ and amyotrophic lateral sclerosis.²⁶ These aggresomes depend on the protein type to be cleared,^{27, 28} and their degradation by autophagy, known as aggrephagy, has been proposed to increase cell viability in neurodegeneration models.²⁹ Interestingly, 4-HNE aggregates have been also found in hepatic cells from alcoholic patients.^{30, 31, 32} Recent data provide no clear cut evidence of a link between PD risk and alcohol consumption with both positive³³ and negative³⁴ results.In this study, we report the cellular effects of EtOH on ARPE-19 cells and determine that EtOH exposure induces the formation of 4-HNE-aggresomes, together with other neurodegenerative hallmarks such as mitochondrial damage and autophagy activation. Considering the central role of RPE in retinal physiology and pathophysiology, and its neural origin, these findings render new insights into the mechanism of neurodegeneration caused by alcohol toxicity in retinal cells, and may contribute to the development of therapeutic strategies in several nervous and retinal diseases.     

The MMS22L-TONSL complex mediates recovery from replication stress and homologous recombination

Genome integrity is jeopardized each time DNA replication forks stall or collapse. Here we report the identification of a complex composed of MMS22L (C6ORF167) and TONSL (NFKBIL2) that participates in the recovery from replication stress. MMS22L and TONSL are homologous to yeast Mms22 and plant Tonsoku/Brushy1, respectively. MMS22L-TONSL accumulates at regions of ssDNA associated with distressed replication forks or at processed DNA breaks, and its depletion results in high levels of endogenous DNA double-strand breaks caused by an inability to complete DNA synthesis after replication fork collapse. Moreover, cells depleted of MMS22L are highly sensitive to camptothecin,?a topoisomerase I poison that impairs DNA replication progression. Finally, MMS22L and TONSL are necessary for the efficient formation of RAD51 foci after DNA damage, and their depletion impairs homologous recombination. These results indicate that MMS22L and TONSL are genome caretakers that stimulate the recombination-dependent repair of stalled or collapsed replication forks.