A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle

Cell cycle control is fundamental in eukaryotic development. Several modeling efforts have been used to integrate the complex network of interacting molecular components involved in cell cycle dynamics. In this paper, we aimed at recovering the regulatory logic upstream of previously known components of cell cycle control, with the aim of understanding the mechanisms underlying the emergence of the cyclic behavior of such components. We focus on Arabidopsis thaliana, but given that many components of cell cycle regulation are conserved among eukaryotes, when experimental data for this system was not available, we considered experimental results from yeast and animal systems. We are proposing a Boolean gene regulatory network (GRN) that converges into only one robust limit cycle attractor that closely resembles the cyclic behavior of the key cell-cycle molecular components and other regulators considered here. We validate the model by comparing our in silico configurations with data from loss- and gain-of-function mutants, where the endocyclic behavior also was recovered. Additionally, we approximate a continuous model and recovered the temporal periodic expression profiles of the cell-cycle molecular components involved, thus suggesting that the single limit cycle attractor recovered with the Boolean model is not an artifact of its discrete and synchronous nature, but rather an emergent consequence of the inherent characteristics of the regulatory logic proposed here. This dynamical model, hence provides a novel theoretical framework to address cell cycle regulation in plants, and it can also be used to propose novel predictions regarding cell cycle regulation in other eukaryotes.     

The turnover of medium-chain-length polyhydroxyalkanoates in Pseudomonas putida KT2442 and the fundamental role of PhaZ depolymerase for the metabolic balance

Polyhydroxyalkanoates (PHAs) are biodegradable polymers produced by a wide range of bacteria, including Pseudomonads. These polymers are accumulated in the cytoplasm as carbon and energy storage materials when culture conditions are unbalanced and hence, they have been classically considered to act as sinks for carbon and reducing equivalents when nutrients are limited. Bacteria facing carbon excess and nutrient limitation store the extra carbon as PHAs through the PHA polymerase (PhaC). Thereafter, under starvation conditions, PHA depolymerase (PhaZ) degrades PHA and releases R -hydroxyalkanoic acids, which can be used as carbon and energy sources. To study the influence of a deficient PHA metabolism in the growth of Pseudomonas putida KT2442 we have constructed two mutant strains defective in PHA polymerase ( phaC1 )- and PHA depolymerase ( phaZ )-coding genes respectively. By using these mutants we have demonstrated that PHAs play a fundamental role in balancing the stored carbon/biomass/number of cells as function of carbon availability, suggesting that PHA metabolism allows P. putida to adapt the carbon flux of hydroxyacyl-CoAs to cellular demand. Furthermore, we have established that the coordination of PHA synthesis and mobilization pathways configures a functional PHA turnover cycle in P. putida KT2442. Finally, a new strain able to secrete enantiomerically pure R -hydroxyalkanoic acids to the culture medium during cell growth has been engineering by redirecting the PHA cycle to biopolymer hydrolysis.     

The crystal structure of a TIR domain from Arabidopsis thaliana reveals a conserved helical region unique to plants

Plants use a highly evolved immune system to exhibit defense response against microbial infections. The plant TIR domain, together with the nucleotide‐binding (NB) domain and/or a LRR region, forms a type of molecule, named resistance (R) proteins, that interact with microbial effector proteins and elicit hypersensitive responses against infection. Here, we report the first crystal structure of a plant TIR domain from Arabidopsis thaliana (AtTIR) solved at a resolution of 2.0 Å. The structure consists of five β‐strands forming a parallel β‐sheet at the core of the protein. The β‐strands are connected by a series of α‐helices and the overall fold mimics closely that of other mammalian and bacterial TIR domains. However, the region of the αD‐helix reveals significant differences when compared with other TIR structures, especially the αD3‐helix that corresponds to an insertion only present in plant TIR domains. Available mutagenesis data suggest that several conserved and exposed residues in this region are involved in the plant TIR signaling function.     

Effects of intermittent aeration periods on a structured-bed reactor continuously fed on the post-treatment of sewage anaerobic effluent

Bioprocess and Biosystems Engineering - This study assessed the simultaneous nitrification and denitrification processes and remaining organic matter removal from anaerobic reactor effluent...     

Nutritional status influences reproductive seasonality in Creole goats: 1. Ovarian activity during seasonal reproductive transitions

The objective was to determine the effect of body energy stores, evaluated by a body mass index (BMI), and food intake (FI), on the length of the anovulatory period and ovarian activity during the seasonal reproductive transitions in Creole goats. Non-pregnant, non-lactating Creole goats (n = 28) were fed to induce two different BMI conditions: Greater (GBMI; n = 15), and Lesser (LBMI; n = 13). Each BMI group was divided into two sub-groups, which were either feed restricted (FR) or non-feed restricted (NFR). Goats in the NFR groups received a diet containing 100% of the daily maintenance requirements (basal diet), while restricted goats were subjected to alternated periods, receiving 100% (11 d) and 60% (10 d) of the basal diet, during the entire experimental period. The experiment started after does were treated to synchronize time of estrus. Serum progesterone was determined in samples obtained twice a week, and used as a criterion for determining ovulations. During the transition to the anovulatory period three transrectal ovarian ultrasonographic scans were performed in a sub-group of 12 goats (n = 3 for each treatment combination). The diameter of the largest follicle (LFD) and the total number of antral follicles ≥2 mm (TAF) were recorded. Ultrasonographic ovarian scans were performed at 21, 42 and 63 days after the beginning of the experiment, concurrently with the end of each feed restriction period. The variables of response associated with ovulation were not influenced by BMI or BMI × FI interaction. However, FI influenced length of anovulatory season, as the anovulatory period was 30 d longer (P < 0.05) in the FR group as compared with the NFR group. Independently of treatments, TAF and LFD decreased from the first to the third ultrasonographic ovarian scan (13.2, 10.8 and 4.4 follicles; 3.7, 2.7 and 2.3 mm). Nevertheless, in PER 1 the number of TAF was greater (P < 0.05) in the FR as compared with NFR group and the GBMI group had a larger LFD (P < 0.05) as compared to the LBMI group. It is concluded, that temporal restriction in feed intake could affect the time of cessation and initiation of ovulations during the periods of transition to seasonal anestrus and return to estrous activity, and increase the length of the anovulatory period. In addition, ovarian follicular development during transition into the anovulatory period is differentially influenced by food intake and the status of body energy stores.     

MAPK signaling to the early secretory pathway revealed by kinase/phosphatase functional screening

To what extent the secretory pathway is regulated by cellular signaling is unknown. In this study, we used RNA interference to explore the function of human kinases and phosphatases in controlling the organization of and trafficking within the secretory pathway. We identified 122 kinases/phosphatases that affect endoplasmic reticulum (ER) export, ER exit sites (ERESs), and/or the Golgi apparatus. Numerous kinases/phosphatases regulate the number of ERESs and ER to Golgi protein trafficking. Among the pathways identified, the Raf–MEK (MAPK/ERK [extracellular signal-regulated kinase] kinase)–ERK cascade, including its regulatory proteins CNK1 (connector enhancer of the kinase suppressor of Ras-1) and neurofibromin, controls the number of ERESs via ERK2, which targets Sec16, a key regulator of ERESs and COPII (coat protein II) vesicle biogenesis. Our analysis reveals an unanticipated complexity of kinase/phosphatase-mediated regulation of the secretory pathway, uncovering a link between growth factor signaling and ER export.     

Study of Poaceae phenology in a Mediterranean climate. Which species contribute most to airborne pollen counts?

The present study sought to determine which of the common Poaceae species in the study area contribute most to the Poaceae pollen season curve, and to determine the phenological behaviour of the species studied. The different floral phenophases in thirty-three Poaceae species common in and around the city of Córdoba (SW Iberian Peninsula) were checked periodically over the period 2004–2006. Results showed that longer phenological ranges were recorded in the coolest and wettest year, and shorter ranges in the warmest and driest year. Moreover, ranges varied as a function of altitude: populations in lower-lying areas flowered earlier than those at higher altitudes. The results, taken in conjunction with the findings of preliminary research into potential pollen production, showed that probably only four of the Poaceae species studied—Dactylis glomerata, Lolium rigidum, Trisetaria panicea and Vulpia geniculata—were major contributors to the Poaceae airborne pollen curve.     

Co-ordinated expression of contractile and non-contractile features of control equine muscle fibre types characterised by immunostaining of myosin heavy chains

Combined methodologies of immunohistochemistry, histochemistry and photometric image analysis were applied: (1) to characterise control equine skeletal muscle fibres according to their myosin heavy chain (MyHC) composition and (2) to determine on a fibre-to-fibre basis the correlation between contractile [i.e. MyHC(s), myofibrillar ATPase (mATPase) and sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) isoforms], metabolic [i.e. succinate dehydrogenase (SDH) and alpha-glycerophosphate dehydrogenase (GPD) activities, glycogen and phospholamban (PLB) contents], and morphological [i.e. cross-sectional area (CSA), capillary and nuclear densities] features of individual myofibres. An accurate delineation of MyHC-based fibre types was obtained with the immunohistochemical method developed. This protocol showed a high sensitivity and objectivity to delineate hybrid fibres with overwhelming dominance of one MyHC isoform and, furthermore, it allowed a semiquantitative delineation of fast hybrid fibres according to the predominant MyHC isoform expressed. The phenotypic differences in contractile, metabolic and morphological properties seen between fibre types were related to MyHC content. Slow fibres had the lowest mATPase activity (related to shortening velocity), the highest SDH activity (oxidative capacity), the lowest GPD activity (glycolytic metabolism) and glycogen content, the smallest CSA, the greatest capillary and nuclear densities, and expressed slow SERCA isoform and PLB, but not the fast SERCA isoform. The reverse pattern was true for pure IID/X fibres, and type IIA fibres had intermediate properties. Hybrid IIAD/X fibres had mean values intermediate to those of their respective pure phenotypes. Discrimination of fibres according to their MyHC content was possible on the basis of their contractile and non-contractile profiles. These intrafibre interdependencies suggest that, even when controlled by different mechanisms, myofibres of control horses exhibit a high degree of co-ordination in their physiological, biochemical and anatomical features.     

GAS6 signaling tempers Th17 development in patients with multiple sclerosis and helminth infection

Multiple sclerosis (MS) is a highly disabling neurodegenerative autoimmune condition in which an unbalanced immune response plays a critical role. Although the mechanisms remain poorly defined, helminth infections are known to modulate the severity and progression of chronic inflammatory diseases. The tyrosine kinase receptors TYRO3, AXL, and MERTK (TAM) have been described as inhibitors of the immune response in various inflammatory settings. We show here that patients with concurrent natural helminth infections and MS condition (HIMS) had an increased expression of the negative regulatory TAM receptors in antigen-presenting cells and their agonist GAS6 in circulating CD11b^high and CD4⁺ T cells compared to patients with only MS. The Th17 subset was reduced in patients with HIMS with a subsequent downregulation of its pathogenic genetic program. Moreover, these CD4⁺ T cells promoted lower levels of the co-stimulatory molecules CD80, CD86, and CD40 on dendritic cells compared with CD4⁺ T cells from patients with MS, an effect that was GAS6-dependent. IL-10⁺ cells from patients with HIMS showed higher GAS6 expression levels than Th17 cells, and inhibition of phosphatidylserine/GAS6 binding led to an expansion of Th17 effector genes. The addition of GAS6 on activated CD4⁺ T cells from patients with MS restrains the Th17 gene expression signature. This cohort of patients with HIMS unravels a promising regulatory mechanism to dampen the Th17 inflammatory response in autoimmunity.     

To Perceive or Not Perceive: The Role of Gamma-band Activity in Signaling Object Percepts

The relation of gamma-band synchrony to holistic perception in which concerns the effects of sensory processing, high level perceptual gestalt formation, motor planning and response is still controversial. To provide a more direct link to emergent perceptual states we have used holistic EEG/ERP paradigms where the moment of perceptual “discovery” of a global pattern was variable. Using a rapid visual presentation of short-lived Mooney objects we found an increase of gamma-band activity locked to perceptual events. Additional experiments using dynamic Mooney stimuli showed that gamma activity increases well before the report of an emergent holistic percept. To confirm these findings in a data driven manner we have further used a support vector machine classification approach to distinguish between perceptual vs. non perceptual states, based on time-frequency features. Sensitivity, specificity and accuracy were all above 95%. Modulations in the 30–75 Hz range were larger for perception states. Interestingly, phase synchrony was larger for perception states for high frequency bands. By focusing on global gestalt mechanisms instead of local processing we conclude that gamma-band activity and synchrony provide a signature of holistic perceptual states of variable onset, which are separable from sensory and motor processing.