Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks

Genome-scale metabolic networks provide a comprehensive structural framework for modeling genotype-phenotype relationships through flux simulations. The solution space for the metabolic flux state of the cell is typically very large and optimization-based approaches are often necessary for predicting the active metabolic state under specific environmental conditions. The objective function to be used in such optimization algorithms is directly linked with the biological hypothesis underlying the model and therefore it is one of the most relevant parameters for successful modeling. Although linear combination of selected fluxes is widely used for formulating metabolic objective functions, we show that the resulting optimization problem is sensitive towards stoichiometry representation of the metabolic network. This undesirable sensitivity leads to different simulation results when using numerically different but biochemically equivalent stoichiometry representations and thereby makes biological interpretation intrinsically subjective and ambiguous. We hereby propose a new method, Minimization of Metabolites Balance (MiMBl), which decouples the artifacts of stoichiometry representation from the formulation of the desired objective functions, by casting objective functions using metabolite turnovers rather than fluxes. By simulating perturbed metabolic networks, we demonstrate that the use of stoichiometry representation independent algorithms is fundamental for unambiguously linking modeling results with biological interpretation. For example, MiMBl allowed us to expand the scope of metabolic modeling in elucidating the mechanistic basis of several genetic interactions in Saccharomyces cerevisiae.     

Cephalopod and brachiopod fossils from the Pacific: Evidence from the Upper Cretaceous of the Magellan Seamounts

Maastrichtian cephalopods and a brachiopod were dredged from the Butakov, Fedorov, Kotsebu, Il’ichev, Govorov, Gelendzhik, and Ita-Mai-Tai guyots in the Magellan Seamounts. The ammonoids Hypophylloceras sp., Phyllopachiceras sp., Anagaudryceras? sp. A, Anagaudryceras? sp. B, Gaudryceras aff. propemite Marshall, Gaudryceras sp., and Pseudophyllites cf. indra (Forbes), and the single brachiopod Basiliolidae gen. and sp. indet. are a first discovery in this oceanic region, following earlier finds of belemnites (Dimitobelus? sp., Dimitobelidae gen. and sp. nov., and Belemnitella? sp.), and two ammonoid species (Zelandites aff. japonicus Matsumoto and Tetragonitidae gen. and sp. indet.). The Late Cretaceous Magellan Seamounts dimitobelid belemnite fauna shows affinities with southern high latitude forms (New Zealand) and the ammonoid fauna with northern, middle and high latitude ones (Hokkaido-Sakhalin and/or Kamchatka). This suggests by the end of the Cretaceous major surface palaeo-currents from S and N sides in direction of the central Palaeo-Pacific, a position coinciding with the plate tectonic reconstruction of the Magellan Seamounts.     

Evaluation Of Atrial Fibrillation Burden Before Catheter Ablation Predicts Outcome After Pulmonary Vein Isolation

Background

Paroxysmal atrial fibrillation (PAF) is defined as recurrent AF terminating spontaneously within 7 days. This definition allows the consideration of any AF occurrence lasting < 7 days as paroxysmal, irrespective of the frequency and duration of episodes. The aim of this study was to investigate symptomatic AF burden (AFB) defined as total duration of symptomatic AF episodes within 3 months prior to abalation, for prediction of outcome after pulmonary vein isolation (PVI).

Methods

A total of 320 consecutive patients with symptomatic AF (PAF=244, men=214, age=58 y) were enrolled. AFB in patients with PAF was defined as time spent in AF within 3 months prior to PVI. After the AFB cut-off point was optimized at 500 h, patients with PAF were categorized into 2 groups: Group 1 - patients with AFB< 500 h (n=192), Group 2 - patients with AFB≥ 500 h (n=52). Patients with persistent AF (PersAF, n = 76) comprised control group (Group 3). PVI was performed either with irrigated tip catheter (n=215) or using cryoballoon (n=105). The endpoint of study was first documented recurrence of AF >30 sec.

Results

Symptomatic AFB was found to be appropriate for prediction of outcome after PVI. The freedom from AF within 2 years was observed in 69%, 31%, and 43% patients in Group 1, 2 and 3, respectively (Group 1 vs. Group 2, p < .001; Group 1 vs. Group 3, p< .001; Group 2 vs. Group 3, p = 0.46).

Conclusions

Low AFB < 500 h /3 months was associated with better outcome after PVI. Patients with PAF and high AFB should be treated as patients with PersAF.     

Invaders are not a random selection of species

We assembled information on 119 species of freshwater macroinvertebrate invaders in North America and Europe, and compared them to all native freshwater species in North America and Europe. We tested whether the invaders were a random or selected group among taxa (phylum or class), water quality requirements, and feeding habit. We found that freshwater macroinvertebrate invaders are not a random selection of species, and are over-represented by molluscs and crustaceans, while taxa richness of native communities are dominated by insects. Over 35% of native species of aquatic invertebrates in North America are only able to live in areas with excellent or very good water quality, and are intolerant of organic pollution. In contrast, all invaders are tolerant of at least moderate amounts of organic pollution. There was a significant difference in the distribution of feeding habits between native species and invaders: collector-filterers (including suspension feeders) were 2.5–3 times more abundant, and predators were 3–4 times less abundant among invaders than among native invertebrates. The ongoing spread of exotic species affects the biodiversity of selected taxa, shifts communities toward greater tolerance of organic pollution and increases the numbers of suspension feeders, thereby enhancing benthic pelagic coupling in waterbodies with high densities of invaders. Because these processes are very similar in Europe and North America, we suggest that the observed patterns may have a common global effect.     

Ecosystem engineering and biodiversity in coastal sediments: posing hypotheses

Coastal sediments in sheltered temperate locations are strongly modified by ecosystem engineering species such as marsh plants, seagrass, and algae as well as by epibenthic and endobenthic invertebrates. These ecosystem engineers are shaping the coastal sea and landscape, control particulate and dissolved material fluxes between the land and sea, and between the benthos and the passing water or air. Above all, habitat engineering exerts facilitating and inhibiting effects on biodiversity. Despite a strongly growing interest in the functional role of ecosystem engineering over the recent years, compared to food web analyses, the conceptual understanding of engineering-mediated species interactions is still in its infancy. In the present paper, we provide a concise overview on current insights and propose two hypotheses on the general mechanisms by which ecosystem engineering may affect biodiversity in coastal sediments. We hypothesise that autogenic and allogenic ecosystem engineers have inverse effects on epibenthic and endobenthic biodiversity in coastal sediments. The primarily autogenic structures of the epibenthos achieve high diversity at the expense of endobenthos, whilst allogenic sediment reworking by infauna may facilitate other infauna and inhibits epibenthos. On a larger scale, these antagonistic processes generate patchiness and habitat diversity. Due to such interaction, anthropogenic influences can strongly modify the engineering community by removing autogenic ecosystem engineers through coastal engineering or bottom trawling. Another source of anthropogenic influences comes from introducing invasive engineers, from which the impact is often hard to predict. We hypothesise that the local biodiversity effects of invasive ecosystem engineers will depend on the engineering strength of the invasive species, with engineering strength defined as the number of habitats it can invade and the extent of modification. At a larger scale of an entire shore, biodiversity need not be decreased by invasive engineers and may even increase. On a global scale, invasive engineers may cause shore biota to converge, especially visually due to the presence of epibenthic structures.     

A procedure to deposit fiducial markers on vitreous cryo-sections for cellular tomography

We describe a novel approach for the accurate alignment of images in electron tomography of vitreous cryo-sections. Quantum dots, suspended in organic solvents at cryo-temperatures, are applied directly onto the sections and are subsequently used as fiducial markers to align the tilt series. Data collection can be performed from different regions of the vitreous sections, even when the sections touch the grid only at a few places. We present high-resolution tomograms of some organelles in cryo-sections of human skin cells using this method. The average error in image alignment was about 1nm and the resolution was estimated to be 5-7nm. Thus, the use of section-attached quantum dots as fiducial markers in electron tomography of vitreous cryo-sections facilitates high-resolution in situ 3D imaging of organelles and macromolecular complexes in their native hydrated state.     

Characterization of AMA, a new AAA protein from Archaeoglobus and methanogenic archaea

We have previously reported a new group of AAA proteins, which is only found in Archaeoglobus and methanogenic archaea (AMA). The proteins are phylogenetically basal to the metalloprotease clade and their N-terminal domain is homologous to the beta-clam part of the N-domain of CDC48-like proteins. Here we report the biochemical and biophysical characterization of Archaeoglobus fulgidus AMA, and of its isolated N-terminal (AMA-N) and ATPase (AMA-DeltaN) domains. AfAMA forms hexameric complexes, as does AMA-N, while AMA-DeltaN only forms dimers. The ability to hexamerize is dependent on the integrity of a GYPL motif in AMA-N, which resembles the pore motif of FtsH and HslU. While the physiological function of AMA is unknown, we show that it has ATP-dependent chaperone activity and can prevent the thermal aggregation of proteins in vitro. The ability to interact with non-native proteins resides in the N-domain and is energy-independent.     

Profiling in basketball: physical and physiological characteristics of elite players

The purpose of this study was to describe structural and functional characteristics of elite Serbian basketball players and to evaluate whether players in different positional roles have different physical and physiological profiles. Five men's basketball teams participated in the study and competed in the professional First National League. Physiological measurements were taken of 60 players during the final week of their preparatory training for competition. According to positional roles, players were categorized as guards (n = 20), forwards (n = 20), and centers (n = 20). Guards were older (p < 0.01) and more experienced (p < 0.01) as compared with both forwards and centers. Centers were taller and heavier than guards and forwards (p < 0.01), whereas forwards had significantly higher height and weight than guards (p < 0.01). Centers had more body fat (p < 0.01) as compared with forwards and guards. Also, centers had significantly lower estimated VO(2)max values (p < 0.01) compared with forwards and guards. In addition, the highest heart rate frequencies during the last minute of the shuttle run test were lower in guards (p < 0.01) as compared with forwards and centers. Vertical jump power was significantly higher in centers (p < 0.01) as compared with guards. The results of the present study demonstrate that a strong relationship exists between body composition, aerobic fitness, anaerobic power, and positional roles in elite basketball.     

Cervical intraepithelial neoplasia: Telomerase activity and splice pattern of hTERT mRNA

Cervical cancers are characterized by the persistence of human papilloma virus (HPV) genome that is found in tissue samples starting from the early stages of tumor progression. Just like in other tumors, the activation of telomerase was observed in cervical carcinomas, but information about its expression was controversial. The aim of this study is to find possible correlations between the presence of HPV sequences, activity of telomerase and expression of different spliced forms of hTERT RNA in cervical intraepithelial neoplasias (CIN). The results show that HPV DNA is present in 60% of normal tissue adjacent to CIN lesions and up to 84% in CIN samples. Telomerase activity was found in 28% of adjacent normal tissue and in 68% of CIN II–III. hTERT RNA that encodes an active enzyme was present almost in all CIN samples. Variations in levels of telomerase activity are possibly not regulated by the splicing forms of hTERT mRNA with deletions.     

Effects of short-term dehydroepiandrosterone supplementation on body composition in young athletes

Dehydroepiandrosterone (DHEA) is often promoted as a slimming and weight/fat loss agent and ingestion of DHEA may have hypolipidemic and anti-obesity properties. The main aim of this study was to examine the effects of acute DHEA intake on body composition and serum steroid hormones in young athletes. Twenty young (19 to 22 years) male soccer players were allocated into two randomly assigned trials in double-blind design by ingesting 100-mg daily oral DHEA or as placebo (PLA) for 28 days. Body mass was not affected by 4 weeks of DHEA supplementation (P > 0.05). No significant changes in body mass index (BMI), waist-to-hip ratio (WHR) and body fat or total muscle mass for the two groups were detected at the end of the trial (P > 0.05). There was no within- or between-group difference in arm fat index (AFI) and corrected mid-upper-arm muscle area (cAMA) (P > 0.05). Treatment with DHEA resulted in a significant increase of total testosterone, estradiol and DHEA-S levels in treated subjects versus the placebo group (P < 0.05). Results of this study suggest that DHEA supplementation has no beneficial effects on body composition in young competitive athletes.