Differential expression analysis for sequence count data

High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.     

The twin-arginine translocation system and its capability for protein secretion in biotechnological protein production

The biotechnological production of recombinant proteins is challenged by processes that decrease the yield, such as protease action, aggregation, or misfolding. Today, the variation of strains and vector systems or the modulation of inducible promoter activities is commonly used to optimize expression systems. Alternatively, aggregation to inclusion bodies may be a desired starting point for protein isolation and refolding. The discovery of the twin-arginine translocation (Tat) system for folded proteins now opens new perspectives because in most cases, the Tat machinery does not allow the passage of unfolded proteins. This feature of the Tat system can be exploited for biotechnological purposes, as expression systems may be developed that ensure a virtually complete folding of a recombinant protein before purification. This review focuses on the characteristics that make recombinant Tat systems attractive for biotechnology and discusses problems and possible solutions for an efficient translocation of folded proteins.     

Purification and characterization of thermostable H<Subscript>2</Subscript>O<Subscript>2</Subscript>-forming NADH oxidase from 2-phenylethanol-assimilating <Emphasis Type="Italic">Brevibacterium</Emphasis> sp. KU1309

A cytoplasmic NADH oxidase (NOX) was purified from a soil bacteria, Brevibacterium sp. KU1309, which is able to grow in the medium containing 2-phenylethanol as the sole source of carbon under an aerobic condition. The enzyme catalyzed the oxidation of NADH to NAD+ involving two-electron reduction of O2 to H2O2. The molecular weight of the enzyme was estimated to be 102 kDa by gel filtration and 57 kDa by SDS-PAGE, which indicates that the NOX was a homodimer consisting of a single subunit. The enzyme was stable up to 70 degrees C at a broad range of pH from 7 to 11. The enzyme activity increased about ten-fold with the addition of ammonium salt, while it was inhibited by Zn2+ (39%), Cu2+ (41%), Hg2+ (72%) and Ag+ (37%). The enzyme acts on NADH, but not on NADPH. The regeneration of NAD+ utilizing this enzyme made selective oxidation of mandelic acid or L: -phenylalanine possible. This thermostable enzyme is expected to be applicable as a useful biocatalyst for NAD+ recycling.     

Aluminum-Induced Cholinergic Deficits in Different Brain Parts and Its Implications on Sociability and Cognitive Functions in Mouse

Aluminum is associated with etiology of many neurodegenerative diseases specially Alzheimer’s disease. Chronic exposure to aluminum via drinking water results in aluminum deposition in the brain that leads to cognitive deficits. The study aimed to determine the effects of aluminum on cholinergic biomarkers, i.e., acetylcholine level, free choline level, and choline acetyltransferase gene expression, and how cholinergic deficit affects novel object recognition and sociability in mice. Mice were treated with AlCl₃ (250 mg/kg). Acetylcholine level, free choline level, and choline acetyltransferase gene expression were determined in cortex, hippocampus, and amygdala. The mice were subjected to behavior tests (novel object recognition and social novelty preference) to assess memory deficits. The acetylcholine level in cortex and hippocampus was significantly reduced in aluminum-treated animals, as compared to cortex and hippocampus of control animals. Acetylcholine level in amygdala of aluminum-treated animals remained unchanged. Free choline level in all the three brain parts was found unaltered in aluminum-treated mice. The novel object recognition memory was severely impaired in aluminum-treated mice, as compared to the control group. Similarly, animals treated with aluminum showed reduced sociability compared to the control mice group. Our study demonstrates that aluminum exposure via drinking water causes reduced acetylcholine synthesis in spite of normal free choline availability. This deficit is caused by reduced recycling of acetylcholine due to lower choline acetyltransferase level. This cholinergic hypofunction leads to cognitive and memory deficits. Moreover, hippocampus is the most affected brain part after aluminum intoxication.     

The effect of jasmonic acid on the accumulation of ABA,proline and spermidine and its influence on membrane injury under water deficit in two barley genotypes

Seedlings of two barley genotypes (‘Maresi’ and wild form of Hordeum spontaneum) were treated with jasmonic acid (JA 5 μM and 15 μM) for 24 h, and then subjected to water stress (PEG 6000 solution of − 1.5 MPa). JA caused an increase in the content of ABA but not in that of proline and spermidine in the two studied genotypes. The effect of the treatment did not depend on the applied JA concentration. The pre-stress treatment with JA changed plant response to water deficit with regard to membrane injury. Treatment with a lower JA concentration (5 μM) caused a substantial reduction of the stress-induced membrane damage in the both genotypes. A higher JA concentration (15 μM) caused the reduction of membrane injury only in H. spontaneum and was ineffective in ‘Maresi’. JA had no influence on the leaf water status in water-stressed plants. A possible role of JA in leaf ABA accumulation and alleviation of cell membrane injury under water deficit is discussed. The work was partly supported by the Polish Committee For Scientific Research, grant No 5 PO6A 036 18     

Immune regulation of bone loss by Th17 cells

A significant macrophage and T-cell infiltrate commonly occurs in inflammatory joint conditions such as rheumatoid arthritis that have significant bone destruction. Cytokines produced by activated macrophages and T cells are implicated in arthritis pathogenesis and are involved in osteoclast-mediated bone resorption. The scope of the present review is to analyze current knowledge and to provide a better understanding of how macrophage-derived factors promote the differentiation of a novel T-helper subset (Th17) that promotes osteoclast formation and activation.     

Associations between primates and other mammals in a central Amazonian forest landscape

Little information exists on mixed-species groups between primates and other mammals in Neotropical forests. In this paper, we describe three such associations observed during an extensive large-vertebrate survey in central Amazonia, Brazil. Mixed-species groups between a primate species and another mammal were observed on seven occasions between squirrel monkeys (Saimiri cf. ustus) and either South American coatis (Nasua nasua) or tayras (Eira barbara) and between brown capuchins (Cebus apella) and coatis. All associations were restricted to floodplain forest during its dry stage. We suggest that the associations involving the coatis are connected to foraging and vigilance but may be induced by a common alternative food resource at a time of food shortage.     

Lessons on Evolution from the Study of Edaphic Specialization

Plants adapted to special soil types are ideal for investigating evolutionary processes, including maintenance of intraspecific variation, adaptation, reproductive isolation, ecotypic differentiation, and the tempo and mode of speciation. Common garden and reciprocal transplant approaches show that both local adaptation and phenotypic plasticity contribute to edaphic (soil-related) specialization. Edaphic specialists evolve rapidly and repeatedly in some lineages, offering opportunities to investigate parallel evolution, a process less commonly documented in plants than in animals. Adaptations to soil features are often under the control of major genes and they frequently have direct or indirect effects on genes that contribute to reproductive isolation. Both reduced competitiveness and greater susceptibility to herbivory have been documented among some edaphic specialists when grown in ‘normal’ soils, suggesting that a high physiological cost of tolerance may result in strong divergent selection across soil boundaries. Interactions with microbes, herbivores, and pollinators influence soil specialization either by directly enhancing tolerance to extremes in soil conditions or by reducing gene flow between divergent populations. Climate change may further restrict the distribution of edaphic specialists due to increased competition from other taxa or, expand their ranges, if preadaptations to drought or other abiotic stressors render them more competitive under a novel climate.     

Auxin-like activity of extract from hypertrophied tissue of <Emphasis Type="Italic">Acacia eburnea</Emphasis> infected with <Emphasis Type="Italic">Ravenelia esculenta</Emphasis>

Ravenelia esculenta Naras. and Thirum. is a rust, pathogenic to Acacia eburnea Willd. The infection leads to hypertrophy changing the morphology with bizarre shapes of plant organs. Healthy and infected tissues were subjected to extraction of IAA and indole derivatives and were estimated by spectrophotometric methods. The hypertrophy produced was presumed to be due to increase in the indole-3-acetic acid (IAA) content in the infected tissue, however, the amount of IAA in infected tissues decreased with the progression of disease. Concomitantly, the infected tissue showed the presence of a novel, slow migrating, indole derivative on TLC. Cultured shoot tips of Withania somnifera were dosed with the methanolic extract of the infected hypertrophied tissue (MEHT) (0.25, 0.5, 0.75, 1.00 and 1.25 mg/l). The stimulation in shoot growth along with profuse rooting was observed in a dose dependent manner with maximum at 1.00 and 1.25 mg/l concentration.     

Evolution of resident bird breeding phenology in a landscape with heterogeneous resource phenology and carryover effects

It is generally expected that, in environments with pronounced seasonal resource peaks, birds’ reproductive success will be maximised when nestlings’ peak food demand coincides with the timing of high food availability. However in certain birds that stay resident over winter, earlier breeding leads juveniles to join the winter flock earlier, which by the prior residence effect increases their success in breeding territory competition. This trade-off between reproduction and competition may explain why, in certain species, breeding phenology is earlier and asynchronous with the resource. This study extends a previous model of the evolution of breeding phenology in a single habitat type to a landscape with two habitat types: ‘early’ and ‘late’ resource phenology. The offspring’s natal habitat type has a carryover effect upon their competitive ability regardless of which habitat type they settle in to potentially breed. We find that, when the difference in resource phenology between habitats is small (weak carryover effect), breeding phenology in the late habitat evolves to occur earlier and more asynchronously than in the early habitat, to compensate for the competitive disadvantage to juveniles raised there. However if the difference is large (strong carryover effect), then the reproductive cost of earlier breeding outweighs the benefit of the compensation, so instead breeding phenology in the late habitat evolves to become more synchronous with the resource. Recruitment is generally asymmetric, from early to late habitat type. However if the early habitat is less frequent in the landscape or produces fewer offspring, then the asymmetry is reduced, and if there is some natal habitat-type fidelity, then recruitment can have an insular pattern, i.e. most recruits to each habitat type come from that same habitat type. We detail the different scenarios in which the different recruitment patterns are predicted, and we propose that they have implications for local adaptation.