Analysis of the Loss in Heat and Acid Resistance during Germination of Spores of Bacillus Species

A major event in the nutrient germination of spores of Bacillus species is release of the spores'' large depot of dipicolinic acid (DPA). This event is preceded by both commitment, in which spores continue through germination even if germinants are removed, and loss of spore heat resistance. The latter event is puzzling, since spore heat resistance is due largely to core water content, which does not change until DPA is released during germination. We now find that for spores of two Bacillus species, the early loss in heat resistance during germination is most likely due to release of committed spores'' DPA at temperatures not lethal for dormant spores. Loss in spore acid resistance during germination also paralleled commitment and was also associated with the release of DPA from committed spores at acid concentrations not lethal for dormant spores. These observations plus previous findings that DPA release during germination is preceded by a significant release of spore core cations suggest that there is a significant change in spore inner membrane permeability at commitment. Presumably, this altered membrane cannot retain DPA during heat or acid treatments innocuous for dormant spores, resulting in DPA-less spores that are rapidly killed.     

Measurement of Force Produced by an Insect-Mimicking Flapping-Wing System

We present a new version of a compact insect-mimicking flapping-wing system driven by a small motor, and suggest two testing approaches to measure the thrust or lift generated by a flapping-wing system. Flapping performance tests show the proposed flapping-wing system, which is powered by an onboard battery (lithium, 3.7 V, 180 mAh), could flap at flapping frequency of 25 Hz, and produce an average thrust or lift of about 3 g. In a wired-flight test under constrained conditions, the flapping-wing system could fly at an average forward velocity of 700 mm·s^?1. For measuring the average thrust or lift produced by the flapping-wing system, we propose two testing approaches of wired-flight test and swing test with the aid of a high-speed camera and they are compared with a load cell measurement. The average thrust or lift values from the two proposed approaches agree well with the average thrust or lift values measured by a load cell.     

Schizophrenia and oxidative stress: glutamate cysteine ligase modifier as a susceptibility gene

Oxidative stress could be involved in the pathophysiology of schizophrenia, a major psychiatric disorder. Glutathione (GSH), a redox regulator, is decreased in patients' cerebrospinal fluid and prefrontal cortex. The gene of the key GSH-synthesizing enzyme, glutamate cysteine ligase modifier (GCLM) subunit, is strongly associated with schizophrenia in two case-control studies and in one family study. GCLM gene expression is decreased in patients' fibroblasts. Thus, GSH metabolism dysfunction is proposed as one of the vulnerability factors for schizophrenia.     

Chemical Components from Phaeanthus vietnamensis and Their Inhibitory NO Production in BV2 Cells

Phaeanthus vietnamensis Bân is a well‐known medicinal plant which has been used for the treatment of various inflammatory diseases in traditional medicine. Using various chromatographic methods, three new compounds, (7S,8R,8′R)‐9,9′‐epoxy‐3,5,3′,5′‐tetramethoxylignan‐4,4′,7‐triol ( 1 ), 8α‐hydroxyoplop‐11(12)‐en‐14‐one ( 5 ), and (1R,2S,4S)‐4‐acetyl‐2‐[(E)‐(cinnamoyloxy)]‐1‐methylcyclohexan‐1‐ol ( 12 ) along with twelve known compounds were isolated from the leaves of P. vietnamensis. Their chemical structures were elucidated by physical and chemical methods. All compounds were evaluated for the inhibitory activities of nitric oxide production in LPS‐stimulated BV2 cells. As the results, compound 6 showed the most potent inhibitory activity on LPS‐stimulated NO production in BV2 cells with the IC₅₀ values of 15.7 ± 1.2 μm . Compounds 2 , 7 , and 8 significantly inhibited inflammatory NO production with IC₅₀ values ranging from 22.6 to 25.3 μm .     

AliSim: A Fast and Versatile Phylogenetic Sequence Simulator for the Genomic Era

Sequence simulators play an important role in phylogenetics. Simulated data has many applications, such as evaluating the performance of different methods, hypothesis testing with parametric bootstraps, and, more recently, generating data for training machine-learning applications. Many sequence simulation programmes exist, but the most feature-rich programmes tend to be rather slow, and the fastest programmes tend to be feature-poor. Here, we introduce AliSim, a new tool that can efficiently simulate biologically realistic alignments under a large range of complex evolutionary models. To achieve high performance across a wide range of simulation conditions, AliSim implements an adaptive approach that combines the commonly used rate matrix and probability matrix approaches. AliSim takes 1.4 h and 1.3 GB RAM to simulate alignments with one million sequences or sites, whereas popular software Seq-Gen, Dawg, and INDELible require 2–5 h and 50–500 GB of RAM. We provide AliSim as an extension of the IQ-TREE software version 2.2, freely available at www.iqtree.org, and a comprehensive user tutorial at http://www.iqtree.org/doc/AliSim.     

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation. A constant adjustment is often used to force the distribution of the intensity log ratios to have a median of zero for each slide. However, such global normalization approaches are not adequate in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. This article proposes normalization methods that are based on robust local regression and account for intensity and spatial dependence in dye biases for different types of cDNA microarray experiments. The selection of appropriate controls for normalization is discussed and a novel set of controls (microarray sample pool, MSP) is introduced to aid in intensity-dependent normalization. Lastly, to allow for comparisons of expression levels across slides, a robust method based on maximum likelihood estimation is proposed to adjust for scale differences among slides.     

Role of liposome on recognition and folding of oxidized and fragmented superoxide dismutase for its re-activation

The behaviors of adsorption and folding of oxidized superoxide dismutase (SOD) fragment on the liposome surface have been studied by varying the type of liposomes. The recognition of the SOD fragment by the liposome was found to be performed, depending on the membrane fluidity, surface charge density and, also, instability of the hydrogen bonds of the liposome surface. The conformational change of the SOD fragment on the liposome membrane was dependent on its adsorption although the variation of their secondary structures was observed. The SOD LIPOzyme (liposome with enzyme-like activity) with high SOD-like activity was obtained by the appropriate control of the recognition and folding of SOD fragment through the suitably-regulated interactions between the liposome and the peptide.     

Screening and preliminary characterization of hemagglutinins in Vietnamese marine algae

Extracts from 44 species of Vietnamese marine algae, including 15 Chlorophyta, 18 Rhodophyta and 11 Phaeophyta species, were examined for hemagglutination activity with a variety of different animal and human erythrocytes that were untreated or treated with enzymes. Almost all extracts showed activity toward at least one type of erythrocytes, although those from three Chlorophyta and two Rhodophyta species showed no hemagglutination with any type of erythrocytes examined. Strong activity was detected in extracts from two Chlorophyta (Anadyomene plicata and Avrainvillea erecta) and four Rhodophyta species (Gracilaria eucheumatoides, Gracilaria salicornia, Kappaphycus alvarezii, and Kappaphycus striatum) with enzyme-treated rabbit and sheep erythrocytes. The hemagglutinins of seven Chlorophyta and eight Rhodophyta species were examined for sugar-binding specificity, pH- and temperature-stability, and divalent cation-independency of hemagglutination using ammonium sulfate-precipitates prepared from their extracts. In a hemagglutination-inhibition test with various monosaccharides and glycoproteins, none of the hemagglutinins had affinity for monosaccharides, except the Codium arabicum and Gracilaria euchematoides hemagglutinins, whose activities were inhibited by both N-acetyl-d-galactosamine and N-acetyl-d-glucosamine. On the other hand, all of the hemagglutinins activities were inhibited by some glycoproteins. The inhibition profiles with glycoproteins were different depending on hemagglutinin species, and suggest the presence of lectins specific for high mannose N-glycans, complex N-glycans, or O-glycans. The activities of these algal hemagglutinins were stable over a wide range of pH and temperature, and independent of the presence of divalent cations. These results indicate that Vietnamese marine algae are a good source of novel and useful lectins.