Genome-wide expression profile of sake brewing yeast under shaking and static conditions

To identify the genes responsible for characteristics, that are different as between sake brewing yeasts and laboratory yeast strains, we used a DNA microarray to compare the genome-wide gene expression profiles of a sake yeast, Saccharomyces cerevisiae K-9 (kyokai 9), and a laboratory yeast, S. cerevisiae X2180-1A, under shaking and static conditions.The genes overexpressed in K-9 more than in X2180-1A were related to C-metabolism, including the HXT, ATP, and COX genes, ergosterol biosynthesis, ERG genes, and thiamine metabolism, THI genes. These genes may contribute to higher growth rates and fermentation ability and the ethanol tolerance of sake yeast.The genes underexpressed in K-9 more than in X2180-1A were CUP1-1 and CUP1-2, PHO genes, which may explain the low copper tolerance and low acid phosphatase activity of sake yeast. These underexpressed genes agree with the features and the alteration of the genome structure of sake yeast.     

Novel mutations affecting axon guidance in zebrafish and a role for plexin signalling in the guidance of trigeminal and facial nerve axons

In zebrafish embryos, the axons of the posterior trigeminal (Vp) and facial (VII) motoneurons project stereotypically to a small number of target muscles derived from the first and second branchial arches (BA1, BA2). Use of the Islet1 (Isl1)-GFP transgenic line enabled precise real-time observations of the growth cone behaviour of the Vp and VII motoneurons within BA1 and BA2. Screening for N-ethyl-N-nitrosourea-induced mutants identified seven distinct mutations affecting different steps in the axonal pathfinding of these motoneurons. The class 1 mutations caused severe defasciculation and abnormal pathfinding in both Vp and VII motor axons before they reached their target muscles in BA1. The class 2 mutations caused impaired axonal outgrowth of the Vp motoneurons at the BA1-BA2 boundary. The class 3 mutation caused impaired axonal outgrowth of the Vp motoneurons within the target muscles derived from BA1 and BA2. The class 4 mutation caused retraction of the Vp motor axons in BA1 and abnormal invasion of the VII motor axons in BA1 beyond the BA1-BA2 boundary. Time-lapse observations of the class 1 mutant, vermicelli (vmc), which has a defect in the plexin A3 (plxna3) gene, revealed that Plxna3 acts with its ligand Sema3a1 for fasciculation and correct target selection of the Vp and VII motor axons after separation from the common pathways shared with the sensory axons in BA1 and BA2, and for the proper exit and outgrowth of the axons of the primary motoneurons from the spinal cord.     

MHC class I molecules are incorporated into human herpesvirus‐6 viral particles and released into the extracellular environment

Human herpesvirus‐6 (HHV‐6), which belongs to the betaherpesvirus subfamily, mainly replicates in T lymphocytes. Here, we show that MHC class I molecules are incorporated into HHV‐6 viral particles and released into the extracellular environment. In addition, HHV‐6A/B‐infected T cells showed reduced surface and intracellular expression of MHC class I molecules. The cellular machinery responsible for molecular transport appears to be modified upon HHV‐6 infection, causing MHC class I molecules to be transported to virion assembly sites.     

Stinging hairs on the Japanese nettle Urtica thunbergiana have a defensive function against mammalian but not insect herbivores

Thorns and hairs of plants can serve as defenses against herbivores, although they may not have evolved under selection by herbivory. Japanese nettles, Urtica thunbergiana, in Nara Park, Nara Prefecture, Japan, where sika deer have been protected for 1200 years, bear many more stinging hairs than those in areas with few or no deer. Previous studies suggested that such hairy nettles evolved under natural selection imposed by intense deer browsing, because stinging hairs deterred deer browsing and because among-population variation in hair density was associated with deer abundance. To confirm this hypothesis, we examined (1) whether stinging hairs affected oviposition and feeding preferences of herbivorous insects and (2) the degree to which they deterred deer via laboratory and field experiments with hairy nettles from Nara Park and with almost-hairless nettles from another area. A specialist butterfly, Indian red admiral, showed no oviposition or larval feeding preferences for either hairy or hairless nettles. Insect damage levels did not significantly differ between the two variants. In contrast, deer browsed hairless nettles more heavily than hairy ones. In hairy nettles, however, the level of deer browsing was not proportional to stinging-hair density, presumably because the hairy nettle population had reached a plateau for resistance as a result of long-term strong directional selection for stinging hairs. These results corroborate the hypothesis that hairy nettles in Nara Park evolved through natural selection under intense deer browsing.     

Three-dimensional culture using human plasma-medium gel with fragmin/protamine microparticles for proliferation of various human cells

Fragmin/protamine microparticles (F/P MPs) have been used as carriers for the preservation and activation of cytokines in human plasma (HP)–Dulbecco’s modified Eagle’s medium (DMEM) gels. This study investigated a three-dimensional (3D) culture system using an HP–DMEM gel with 0.1 mg/mL F/P MPs and 5 ng/mL FGF-2 for the proliferation of human dermal fibroblast cells (DFCs), human microvascular endothelial cells (MVECs) and human coronary smooth muscle cells (SMCs), or 5 ng/mL interleukin (IL)-3/granulocyte-macrophage colony-stimulating factor (GM-CSF) for a human hematopoietic cell line (TF-1 cells). DFCs, MVECs, SMCs and TF-1 cells grew rapidly under 3D culture conditions using a low-concentration HP (2 %)–DMEM gel with F/P MPs and FGF-2 (for DFCs, MVECs and SMCs) or IL-3/GM-CSF (for TF-1 cells) at doubling times of 22, 23, 25 and 18 h, respectively, without the use of animal serum, compared to under 2D culture conditions using low-concentration human serum (2 %)–DMEM with 5 ng/mL FGF-2 or IL-3/GM-CSF on F/P MP-coated plates at doubling times of approximately 26, 25, 40 and 20 h, respectively.     

Endophytic and mycorrhizal fungi associated with roots of endangered native orchids from the Atlantic Forest, Brazil

The composition and diversity of fungal communities associated with three endangered orchid species, Hadrolaelia jongheana, Hoffmannseggella caulescens, and Hoffmannseggella cinnabarina, found in different vegetation formations of the Atlantic Forest were determined by constructing clone libraries and by applying diversity and richness indices. Our results demonstrated the presence of Basidiomycetes. Sebacinales (81.61 %) and Cantharellales (12.10 %) were the dominant orders and are potential candidates for orchid mycorrhizal fungi. The Ascomycetes identified included the Helotiales (29.31 %), Capnodiales (18.10 %), and Sordariales (10.34 %), among others. These orders may represent potentially endophytic fungi. A Shannon–Wiener diversity index (H′) analysis showed a relatively high fungal community diversity associated with these tropical orchids. This diversity may offer greater flexibility in terms of the adaptation of the plants to changing environmental conditions and the potential facilitation of reintroduction programs. The Simpson diversity index values showed that all of the libraries included dominant species, and a LIBSHUFF analysis showed that the fungal communities were structurally different from each other, suggesting an influence of local factors on this diversity. This study offers important information for the development of conservation strategies for threatened and endemic species of Brazilian flora in an important and threatened hotspot.     

Protective Efficacy of Passive Immunization with Monoclonal Antibodies in Animal Models of H5N1 Highly Pathogenic Avian Influenza Virus Infection

Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype often cause severe pneumonia and multiple organ failure in humans, with reported case fatality rates of more than 60%. To develop a clinical antibody therapy, we generated a human-mouse chimeric monoclonal antibody (MAb) ch61 that showed strong neutralizing activity against H5N1 HPAI viruses isolated from humans and evaluated its protective potential in mouse and nonhuman primate models of H5N1 HPAI virus infections. Passive immunization with MAb ch61 one day before or after challenge with a lethal dose of the virus completely protected mice, and partial protection was achieved when mice were treated 3 days after the challenge. In a cynomolgus macaque model, reduced viral loads and partial protection against lethal infection were observed in macaques treated with MAb ch61 intravenously one and three days after challenge. Protective effects were also noted in macaques under immunosuppression. Though mutant viruses escaping from neutralization by MAb ch61 were recovered from macaques treated with this MAb alone, combined treatment with MAb ch61 and peramivir reduced the emergence of escape mutants. Our results indicate that antibody therapy might be beneficial in reducing viral loads and delaying disease progression during H5N1 HPAI virus infection in clinical cases and combined treatment with other antiviral compounds should improve the protective effects of antibody therapy against H5N1 HPAI virus infection.     

Contact Doping with Sub‐Monolayers of Strong Polyelectrolytes for Organic Photovoltaics

Barriers to charge transfer at electrode‐semiconductor contacts are ubiquitous and limit the applicability of organic semiconductors in electronic devices. Molecular or ionic doping near contacts can alleviate charge injection or extraction problems by enabling charge tunneling through contact barriers, but the soft nature of organic materials allows for small molecule dopants to diffuse and migrate, degrading the performance of the device and limiting effective interfacial doping. Here, it is demonstrated that contact doping in organic electronics is possible through ionic polymer dopants, which resist diffusion or migration due to their large size. Sub‐monolayer deposition of non‐conjugated strong polyelectrolytes, e.g., sulfonated poly(sulfone)s, at the anode‐semiconductor interface of organic photovoltaics enables efficient hole extraction at the anode. The performance of contact‐doped organic photo­voltaics nearly matches the performance of devices composed of traditional hole transport layers such as poly(3,4‐ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS). The degree of sulfonation of the dopant polymer and the thickness of the ionic dopant layer is shown to be critical for optimizing doping and the efficiency of the device.     

Abiotic and Biotic Degradation of Oxo-Biodegradable Plastic Bags by Pleurotus ostreatus

In this study, we evaluated the growth of Pleurotus ostreatus PLO6 using oxo-biodegradable plastics as a carbon and energy source. Oxo-biodegradable polymers contain pro-oxidants that accelerate their physical and biological degradation. These polymers were developed to decrease the accumulation of plastic waste in landfills. To study the degradation of the plastic polymers, oxo-biodegradable plastic bags were exposed to sunlight for up to 120 days, and fragments of these bags were used as substrates for P. ostreatus. We observed that physical treatment alone was not sufficient to initiate degradation. Instead, mechanical modifications and reduced titanium oxide (TiO₂) concentrations caused by sunlight exposure triggered microbial degradation. The low specificity of lignocellulolytic enzymes and presence of endomycotic nitrogen-fixing microorganisms were also contributing factors in this process.