Timing Robustness in the Budding and Fission Yeast Cell Cycles

Robustness of biological models has emerged as an important principle in systems biology. Many past analyses of Boolean models update all pending changes in signals simultaneously (i.e., synchronously), making it impossible to consider robustness to variations in timing that result from noise and different environmental conditions. We checked previously published mathematical models of the cell cycles of budding and fission yeast for robustness to timing variations by constructing Boolean models and analyzing them using model-checking software for the property of speed independence. Surprisingly, the models are nearly, but not totally, speed-independent. In some cases, examination of timing problems discovered in the analysis exposes apparent inaccuracies in the model. Biologically justified revisions to the model eliminate the timing problems. Furthermore, in silico random mutations in the regulatory interactions of a speed-independent Boolean model are shown to be unlikely to preserve speed independence, even in models that are otherwise functional, providing evidence for selection pressure to maintain timing robustness. Multiple cell cycle models exhibit strong robustness to timing variation, apparently due to evolutionary pressure. Thus, timing robustness can be a basis for generating testable hypotheses and can focus attention on aspects of a model that may need refinement.     

Diversity of lactic acid bacteria of the bioethanol process

Background  

Bacteria may compete with yeast for nutrients during bioethanol production process, potentially causing economic losses. This is the first study aiming at the quantification and identification of Lactic Acid Bacteria (LAB) present in the bioethanol industrial processes in different distilleries of Brazil.     

Influence of sea buckthorn (Hippophae rhamnoides L.) flavone on dermal wound healing in rats

The present investigation was undertaken to determine the efficacy of topical administration of flavone of sea buckthorn (Hippophae rhamnoides L.) on cutaneous wound healing in rats. Four full-thickness excision wounds were created on the back of rat and 1.0% w/v flavone prepared in propylene glycol was applied topically. Control animals received the vehicle alone in an identical manner. The healing of the wound was assessed by the rate of wound contraction, period of epithelialization, hydroxyproline, hexosamine, antioxidants estimation and histopathology of the granulation tissue. The sea buckthorn flavone promoted the wound healing activity as indicated by improved rate of wound contraction, decreased time taken for epithelialization (16.3 days versus 24.8 days in controls) and significant increase in hydroxyproline (26.0%) and hexosamine (30.0%) content. These findings were also confirmed by histopathological examinations. In addition, it was observed that sea buckthorn flavone possesses potent antioxidant properties as evidenced by significant increase in reduced glutathione (55.0%), vitamin C (70.0%) and catalase (20.0%) activities in wound granulation tissue. The flavone treatment also resulted in significant decrease in lipid peroxide levels (39.0%). The results suggest that the sea buckthorn flavone promotes wound healing activity.     

Overexpression of a nascent polypeptide associated complex gene (SaβNAC) of Spartina alterniflora improves tolerance to salinity and drought in transgenic Arabidopsis

Salinity and drought are the most important environmental constraints limiting crop growth and productivity. Here, we have characterized a gene 'SaβNAC' encoding the β subunit of nascent polypeptide associated complex from a halophyte Spartina alterniflora and investigated its role toward abiotic stress regulation. Expression of SaβNAC was differentially regulated by abiotic stresses, including salinity, drought, cold, and ABA in leaves and roots of S. alterniflora. Constitutive over-expression of SaβNAC in Arabidopsis exhibited normal growth under non-stress conditions but enhanced tolerance to salt and drought stresses. Transgenic SaβNAC Arabidopsis retained more chlorophyll, proline, and showed improved ionic homeostasis with less damage under stress conditions compared to WT plants. This is a first report to demonstrate the involvement of βNAC in imparting abiotic stress tolerance which might be due to protection of the newly synthesized polypeptides involved in various stress tolerance mechanisms from abiotic stress induced damage and inhibition of cell death in plant.     

Optimization of cellulase-free xylanase production by alkalophilic Cellulosimicrobium sp. CKMX1 in solid-state fermentation of apple pomace using central composite design and response surface methodology

Microbial xylanases and associated enzymes degrade the xylans present in lignocellulose in nature. Xylanase production by Cellulosimicrobium sp. CKMX1, isolated from mushroom compost, produced a cellulase-free extracellular endo-1, 4-β-xylanase (EC 3.2.1.8) at 35 °C and pH 8.0. Apple pomace—an inexpensive and abundant source of carbon—supported maximal xylanase activity of 500.10 U/g dry bacterial pomace (DBP) under solid state fermentation. Culture conditions, e.g., type of medium, particle size of carbon source, incubation period, temperature, initial pH, and inoculum size, were optimized and xylanase activity was increased to 535.6 U/g DBP. CMCase, avicelase, FPase and β-glucosidase activities were not detected, highlighting the novelty of the xylanase enzyme produced by CKMX1. Further optimization of enzyme production was carried out using central composite design following response surface methodology with four independent variables (yeast extract, urea, Tween 20 and carboxymethyl cellulose), which resulted in very high levels of xylanase (861.90 U/g DBP). Preliminary identification of the bacterial isolate was made on the basis of morphological and biochemical characters and confirmed by partial 16Sr RNA gene sequencing, which identified CKMX1 as Cellulosimicrobium sp. CKMX1. A phylogenetic analysis based on the 16Sr RNA gene sequence placed the isolate within the genus Cellulosimicrobium, being related most closely to Cellulosimicrobium cellulans strain AMP-11 (97% similarity). The ability of this strain to produce cost-effective xylanase from apple pomace on a large scale will help in the waste management of apple pomace.     

Limitations of trait‐based approaches for stressor assessment: The case of freshwater invertebrates and climate drivers

The appeal of trait‐based approaches for assessing environmental vulnerabilities arises from the potential insight they provide into the mechanisms underlying the changes in populations and community structure. Traits can provide ecologically based explanations for observed responses to environmental changes, along with predictive power gained by developing relationships between traits and environmental variables. Despite these potential benefits, questions remain regarding the utility and limitations of these approaches, which we explore focusing on the following questions: (a) How reliable are predictions of biotic responses to changing conditions based on single trait–environment relationships? (b) What factors constrain detection of single trait–environment relationships, and how can they be addressed? (c) Can we use information on meta‐community processes to reveal conditions when assumptions underlying trait‐based studies are not met? We address these questions by reviewing published literature on aquatic invertebrate communities from stream ecosystems. Our findings help to define factors that influence the successful application of trait‐based approaches in addressing the complex, multifaceted effects of changing climate conditions on hydrologic and thermal regimes in stream ecosystems. Key conclusions are that observed relationships between traits and environmental stressors are often inconsistent with predefined hypotheses derived from current trait‐based thinking, particularly related to single trait–environment relationships. Factors that can influence findings of trait‐based assessments include intercorrelations of among traits and among environmental variables, spatial scale, strength of biotic interactions, intensity of habitat disturbance, degree of abiotic stress, and methods of trait characterization. Several recommendations are made for practice and further study to address these concerns, including using phylogenetic relatedness to address intercorrelation. With proper consideration of these issues, trait‐based assessment of organismal vulnerability to environmental changes can become a useful tool to conserve threatened populations into the future.     

High-Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells

H1 linker histones facilitate higher-order chromatin folding and are essential for mammalian development. To achieve high-resolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H1⁰ displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d, and H1e causes pericentric chromocenter clustering and de-repression of major satellites. These results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and we identify significant changes at pericentric heterochromatin upon depletion of this epigenetic mark.     

Synthesis,Characterization, and Structural Modeling of High‐Capacity,Dual Functioning MnO2 Electrode/Electrocatalysts for Li‐O2 Cells

It has become clear that cycling lithium‐oxygen cells in carbonate electrolytes is impractical, as electrolyte decomposition, triggered by oxygen reduction products, dominates the cell chemistry. This research shows that employing an α‐MnO₂/ramsdellite‐MnO₂ electrode/electrocatalyst results in the formation of lithium‐oxide‐like discharge products in propylene carbonate, which has been reported to be extremely susceptible to decomposition. X‐ray photoelectron data have shown that what are likely lithium oxides (Li₂O₂ and Li₂O) appear to form and decompose on the air electrode surface, particularly at the MnO₂ surface, while Li₂CO₃ is also formed. By contrast, cells without α‐MnO₂/ramsdellite‐MnO₂ fail rapidly in electrochemical cycling, likely due to the differences in the discharge product. Relatively high electrode capacities, up to 5000 mAh/g (carbon + electrode/electrocatalyst), have been achieved with non‐optimized air electrodes. Insights into reversible insertion reactions of lithium, lithium peroxide (Li₂O₂) and lithium oxide (Li₂O) in the tunnels of α‐MnO₂, and the reaction of lithium with ramsdellite‐MnO₂, as determined by first principles density functional theory calculations, are used to provide a possible explanation for some of the observed results. It is speculated that a Li₂O‐stabilized and partially‐lithiated electrode component, 0.15Li₂O·α‐Li_xMnO₂, that has Mn^4+/3+ character may facilitate the Li₂O₂/Li₂O discharge/charge chemistries providing dual electrode/electrocatalyst functionality.     

Fibre bundle element method of determining physiological cross-sectional area from three-dimensional computer muscle models created from digitised fibre bundle data

Physiological cross-sectional area (PCSA) is used to compare force-producing capabilities of muscles. A limitation of PCSA is that it cannot be measured directly from a specimen, as there is usually no area within the muscle traversed by all fibres. Traditionally, a formula requiring averaged architectural parameters has been used. The purpose of this paper is to describe the development of a fibre bundle element (FBE) method to calculate PCSA from digitised fibre bundle data of five architecturally distinct muscles and compare the FBE and PCSA formula. An FBE method was developed that used a serially arranged set of cylinders as the volumetric representation of each fibre bundle, and PCSA was computed as the summation of the cross-sectional area of each FBE. Four of five muscles had significantly different PCSA between FBE and formula methods. The FBE method provides an approach that considers architectural variances while minimising the need for averaged architectural parameters.