<Emphasis Type="Italic">Achromobacter panacis</Emphasis> sp. nov., isolated from rhizosphere of <Emphasis Type="Italic">Panax ginseng</Emphasis>

A novel strain DCY105^T was isolated from soil collected from the rhizosphere of ginseng (Panax ginseng), in Gochang, Republic of Korea. Strain DCY105^T is Gram-reaction-negative, white, non-motile, non-flagellate, rod-shaped and aerobic. The bacteria grow optimally at 30°C, pH 6.5–7.0 and in the absence of NaCl. Phylogenetically, strain DCY105^T is most closely related to Achromobacter marplatensis LMG 26219^T (96.81%). The DNA G+C content of strain DCY105^T was 64.4 mol%. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were amongst the major polar lipids. C_16:00, C_8:03OH and iso-C_17:03OH were identified as the major fatty acids present in DCY105^T. The results of physiological and biochemical tests allowed strain DCY105^T to be differentiated phenotypically from other recognized species belonging to the genus Achromobacter. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Achromobacter panacis sp. nov. is proposed with the type strain designated as DCY105^T (=CCTCCAB 2015193^T =KCTC 42751^T).     

Extraocular vision in the sea urchin Diadema setosum

In most organisms, specific structures are responsible for detecting light patterns and vision. Several species of sea urchins appear to have a diffuse photoreceptor system that enables them to detect light and in some cases objects. The presence of extraocular vision was investigated on a sea urchin common in northern Oman, Diadema setosum. Urchins from 8- to 10-m deep coral communities were used in controlled experiments that quantified the orientation response of the urchins to various visual cues: size, contrast and colour of circular targets simulating urchins’ outlines. Urchins responded to black discs down to 11° initial visual angle but not to smaller discs. The minimum grey-scale value triggering a response was between 50 and 37% black. Urchins responded to red targets but not to green or blue ones. An average angular distance between spines of 5.3° suggested a visual acuity of about 10.6°. D. setosum thus showed extraocular vision allowing them to detect objects of different sizes, contrasts and to some extent colour, supporting the hypothesis that the whole sea urchin’s body acts as a single large compound eye.     

Biotransformation of prednisolone to hydroxy derivatives by Penicillium aurantiacum

Prednisolone, a synthetic adrenal corticosteroid drug, is known to have anti-inflammatory and autoimmune activity. Biotransformation of prednisolone was carried out to obtain more bioactive prednisolone derivatives. Among six different fungi, Penicillium aurantiacum proved to be the best prednisolone hydroxylator. As a result of prednisolone biotransformation by P. aurantiacum, whole cells four different prednisolone derivatives were investigated. 20β-Hydroxyprednisolone (1) and 21,21-dimethoxy-11β-hydroxypregn-1,4-dien-3,20-dione (2) were detected as the main metabolites. These metabolites together with other two metabolites, 11β-hydroxyandrost-1,4-dien-3,17-dione (3) and 11β,17β-dihydroxyandrost-1,4-dien-3- one (4), were purified and assigned by an interpretation of their spectral data using mass spectroscopy (MS), proton nuclear magnetic resonance (¹H-NMR), carbon nuclear magnetic resonance (¹³C-NMR) and infrared spectroscopy (IR) analyses. The best fermentation conditions for production of compounds 1–4 were as follows: medium (3) consisting of (g/l): glucose 20; l-asparagine 0.7; MgSO₄.7H₂O 0.5; KH₂PO₄ 1.52; KCl 0.52; Cu (NO₃)₂ traces; ZnSO₄.7H₂O traces, supplemented with prednisolone concentration of 0.3?mg/ml, inoculated by 10% of microorganism and incubated for 72?h. Under these optimized conditions, ～94.8% of the added prednisolone was converted to aforementioned derivatives, which have the potential to be used in industrial production of important pharmaceutical compounds.     

Properties of STAT1 and IRF1 enhancers and the influence of SNPs

Background

STAT1 and IRF1 collaborate to induce interferon-γ (IFNγ) stimulated genes (ISGs), but the extent to which they act alone or together is unclear. The effect of single nucleotide polymorphisms (SNPs) on in vivo binding is also largely unknown.

Results

We show that IRF1 binds at proximal or distant ISG sites twice as often as STAT1, increasing to sixfold at the MHC class I locus. STAT1 almost always bound with IRF1, while most IRF1 binding events were isolated. Dual binding sites at remote or proximal enhancers distinguished ISGs that were responsive to IFNγ versus cell-specific resistant ISGs, which showed fewer and mainly single binding events. Surprisingly, inducibility in one cell type predicted ISG-responsiveness in other cells. Several dbSNPs overlapped with STAT1 and IRF1 binding motifs, and we developed methodology to rapidly assess their effects. We show that in silico prediction of SNP effects accurately reflects altered binding both in vitro and in vivo.

Conclusions

These data reveal broad cooperation between STAT1 and IRF1, explain cell type specific differences in ISG-responsiveness, and identify genetic variants that may participate in the pathogenesis of immune disorders.

     

Legume Protein Isolates for Stable Acidic Emulsions Prepared by Premix Membrane Emulsification

Proteins originating from dry legumes are not that much used in food formulations, yet, they are interesting components from a sustainability point of view, and could have interesting functional properties, e.g. for emulsion preparation. Therefore, this work focuses on the potential of the water soluble part of pea, chickpea and lentil protein isolates under acidic emulsions (pH 3.0) using a novel mild technique: premix membrane emulsification. Pea proteins (PP) and chickpea proteins (CP) lower the interfacial tension in the same way as whey protein isolate (WPI), which suggests that they could facilitate emulsion droplet formation similarly as WPI, while lentil proteins (LP) are slightly less effective. It is possible to make oil-in-water (O/W) emulsions with an average droplet diameter (d _4,3 ) of ~5 μm after 5 cycles in the premix system. The droplet size distribution of the emulsions remained constant during one day of storage, indicating that legume proteins are able to form and kinetically stabilize O/W emulsions. CP and PP exhibited emulsifying properties comparable to those of WPI, whereas LP is slightly less efficient, therewith indicating the great potential and that pea and chickpea protein isolates hold as emulsifiers in acidic food formulations.     

Wettability,Polarity, and Water Absorption of Holm Oak Leaves: Effect of Leaf Side and Age

Plant trichomes play important protective functions and may have a major influence on leaf surface wettability. With the aim of gaining insight into trichome structure, composition, and function in relation to water-plant surface interactions, we analyzed the adaxial and abaxial leaf surface of holm oak (Quercus ilex) as a model. By measuring the leaf water potential 24 h after the deposition of water drops onto abaxial and adaxial surfaces, evidence for water penetration through the upper leaf side was gained in young and mature leaves. The structure and chemical composition of the abaxial (always present) and adaxial (occurring only in young leaves) trichomes were analyzed by various microscopic and analytical procedures. The adaxial surfaces were wettable and had a high degree of water drop adhesion in contrast to the highly unwettable and water-repellent abaxial holm oak leaf sides. The surface free energy and solubility parameter decreased with leaf age, with higher values determined for the adaxial sides. All holm oak leaf trichomes were covered with a cuticle. The abaxial trichomes were composed of 8% soluble waxes, 49% cutin, and 43% polysaccharides. For the adaxial side, it is concluded that trichomes and the scars after trichome shedding contribute to water uptake, while the abaxial leaf side is highly hydrophobic due to its high degree of pubescence and different trichome structure, composition, and density. Results are interpreted in terms of water-plant surface interactions, plant surface physical chemistry, and plant ecophysiology.Plant surfaces have an important protecting function against multiple biotic and abiotic stress factors (Riederer, 2006). They may, for example, limit the attack of insects (Eigenbrode and Jetter, 2002) or pathogenic fungi (Gniwotta et al., 2005; Łaźniewska et al., 2012), avoid damage caused by high intensities of UV and visible radiation (Reicosky and Hanover, 1978; Karabourniotis and Bormann, 1999), help to regulate leaf temperature (Ehleringer and Björkman, 1978; Ripley et al., 1999), and chiefly prevent plant organs from dehydration (Riederer and Schreiber, 2001).The epidermis of plants has been found to have a major degree of physical and chemical variability and may often contain specialized cells such as trichomes or stomata (Roth-Nebelsick et al., 2009; Javelle et al., 2011). Most aerial organs are covered with an extracellular and generally lipid-rich layer named the cuticle, which is typically composed of waxes embedded in (intracuticular waxes) or deposited on (epicuticular waxes) a biopolymer matrix of cutin, forming a network of cross-esterified hydroxy C₁₆ and/or C₁₈ fatty acids, and/or cutan, with variable amounts of polysaccharides and phenolics (Domínguez et al., 2011; Yeats and Rose, 2013). Different nano- and/or microscale levels of plant surface sculpturing have been observed by scanning electron microscopy (SEM), generally in relation to the topography of epicuticular waxes, cuticular folds, and epidermal cells (Koch and Barthlott, 2009). Such surface features together with their chemical composition (Khayet and Fernández, 2012) may lead to a high degree of roughness and hydrophobicity (Koch and Barthlott, 2009; Konrad et al., 2012). The interactions of plant surfaces with water have been addressed in some investigations (Brewer et al., 1991; Brewer and Smith, 1997; Pandey and Nagar, 2003; Hanba et al., 2004; Dietz et al., 2007; Holder, 2007a, 2007b; Fernández et al., 2011, 2014; Roth-Nebelsick et al., 2012; Wen et al., 2012; Urrego-Pereira et al., 2013) and are a topic of growing interest for plant ecophysiology (Helliker and Griffiths, 2007; Aryal and Neuner, 2010; Limm and Dawson, 2010; Kim and Lee, 2011; Berry and Smith, 2012; Berry et al., 2013; Rosado and Holder, 2013; Helliker, 2014). On the other hand, the mechanisms of foliar uptake of water and solutes by plant surfaces are still not fully understood (Fernández and Eichert, 2009; Burkhardt and Hunsche, 2013), but they may play an important ecophysiological role (Limm et al., 2009; Johnstone and Dawson, 2010; Adamec, 2013; Berry et al., 2014).The importance of trichomes and pubescent layers on water drop-plant surface interactions and on the subsequent potential water uptake into the organs has been analyzed in some investigations (Fahn, 1986; Brewer et al., 1991; Grammatikopoulos and Manetas, 1994; Brewer and Smith, 1997; Pierce et al., 2001; Kenzo et al., 2008; Fernández et al., 2011, 2014; Burrows et al., 2013). Trichomes are unicellular or multicellular and glandular or nonglandular appendages, which originate from epidermal cells only and develop outwards on the surface of plant organs (Werker, 2000). Nonglandular trichomes are categorized according to their morphology and exhibit a major variability in size, morphology, and function. On the other hand, glandular trichomes are classified by the secretory materials they excrete, accumulate, or absorb (Johnson, 1975; Werker, 2000; Wagner et al., 2004). Trichomes can be often found in xeromorphic leaves and in young organs (Fahn, 1986; Karabourniotis et al., 1995). The occurrence of protecting leaf trichomes has been also reported for Mediterranean species such as holm oak (Quercus ilex; Karabourniotis et al., 1995, 1998; Morales et al., 2002; Karioti et al., 2011; Camarero et al., 2012). There is limited information about the nature of the surface of trichomes, but they are also covered with a cuticle similarly to other epidermal cell types (Fernández et al., 2011, 2014).In this study and using holm oak as a model, we assessed, for the first time, the leaf surface-water relations of the abaxial (always pubescent) versus the adaxial (only pubescent in developing leaves and for a few months) surface, including their capacity to absorb surface-deposited water drops. Based on membrane science methodologies (Fernández et al., 2011; Khayet and Fernández, 2012) and following a new integrative approach, the chemical, physical, and anatomical properties of holm oak leaf surfaces and trichomes were analyzed, with the aim of addressing the following questions. Are young and mature adaxial and abaxial leaf surfaces capable of absorbing water deposited as drops on to the surfaces? Are young and mature abaxial and adaxial leaf surfaces similar in relation to their wettability, hydrophobicity, polarity, work of adhesion (W_a) for water, solubility parameter (δ), and surface free energy (γ)? What is the physical and chemical nature of the adaxial versus the abaxial trichomes, chiefly in relation to young leaves?     

A whole mitochondrial genome screening in a MELAS patient: a novel mitochondrial tRNA(Val) mutation

Mitochondrial encephalopathy, lactic acidosis and strokelike episodes (MELAS) syndrome is a mitochondrial disorder characterized by a wide variety of clinical presentations and a multisystemic organ involvement. In this study, we report a Tunisian girl with clinical features of MELAS syndrome who was negative for the common m.3243A>G mutation, but also for the reported mitochondrial DNA (mtDNA) mutations and deletions. Screening of the entire mtDNA genome showed several known mitochondrial variants besides to a novel transition m.1640A>G affecting a wobble adenine in the anticodon stem region of the tRNA(Val). This nucleotide was conserved and it was absent in 150 controls suggesting its pathogenicity. In addition, no mutations were found in the nuclear polymerase gamma-1 gene (POLG1). These results suggest further investigation nuclear genes encoding proteins responsible for stability and structural components of the mtDNA or to the oxidative phosphorylation machinery to explain the phenotypic variability in the studied family.     

Complete genome sequence of the obligate piezophilic hyperthermophilic archaeon Pyrococcus yayanosii CH1

Pyrococcus yayanosii CH1 is the first obligate piezophilic hyperthermophilic archaeon isolated from the deep-sea hydrothermal site Ashadze on the mid-Atlantic ridge at a depth of 4,100 m. This organism grows within a temperature range of 80 to 108°C and a hydrostatic pressure range of 20 to 120 MPa, with optima at 98°C and 52 MPa, respectively. Here, we report the complete genome sequence (1,716,817 bp, with a G+C content of 51.6%) of the type strain P. yayanosii CH1(T) (= JCM 16557). This genomic information reveals a systematic view of the piezoadaptation strategy and evolution scenario of metabolic pathways in Thermococcales.