Yeasts as models in evolutionary biology

A report of the workshop 'Evolutionary and Environmental Genomics of Yeasts', Heidelberg, Germany, 1-5 October 2008.     

Yeasts that ferment D-cellobiose as well as D-xylose

Summary Yeasts that ferment both D-cellobiose and D-xylose have been identified. Such organisms may have advantages in the simultaneous saccharification and fermentation of cellulosics by obviating D-cellobiose inhibition of cellulase activity, and by allowing concurrent processing of the hemicellulose and cellulose.     

Distillery and curd whey wastes as viable alternative sources for biosurfactant production

Biosurfactant production from synthetic medium and industrial waste, viz. distillery and whey wastes was investigated by using an oily sludge isolate Pseudomonas aeruginosa strain BS2. In synthetic medium separately supplemented with glucose and hexadecane as water-soluble and -insoluble carbon sources, respectively, strain BS2 reduced the surface tension of the fermentation broth from 57 to 27 mN/m. The culture produced biosurfactant during the stationary growth phase and its yield was 0.97 g/l. The culture utilized distillery and whey wastes for its growth, as maximum cell counts reached to 54 × 10⁸ and 64 × 10⁹ c.f.u./ml from an initial inoculum size of 1 × 0⁵ c.f.u./ml, respectively, within 48 h of incubation and in these wastes the yields of biosurfactant obtained were 0.91 and 0.92 g/l, respectively. In synthetic medium, distillery and whey wastes, strain BS2 produced a crystalline biosurfactant which belonged to the category of secondary metabolites and its maximum production occurred after the onset of nitrogen-limiting conditions. After recovering biosurfactant from the fermented waste, the chemical oxygen demand (COD) of distillery and whey wastes was significantly reduced by 81 and 87%, respectively. Total acids, nitrogen and phosphate levels in distillery waste were reduced by 90, 92 and 92%, respectively, while in case of whey waste the concentration of these nutrients was reduced by 88, 95 and 93%, respectively. The isolated biosurfactant possessed potent surface active properties, as it effectively reduced the surface tension of water from 72 to 27 mN/m and formed 100% stable emulsions of a variety of water-insoluble compounds such as hydrocarbons, viz. hexadecane, crude oil, kerosene and oily sludge and pesticides, viz. dichlorodiphenyltrichloroethane (DDT) and benzene hexachloride (BHC). The effectiveness of biosurfactant was also evident from its low critical micellar concentration (CMC) which was 0.028 mg/ml.     

Engineered Yeasts as Reporter Systems for Odorant Detection

Abstract

The functional expression of olfactory receptors (ORs) is a primary requirement to utilize olfactory detection systems. We have taken advantage of the functional similarities between signal transduction cascades in the budding yeast Saccharomyces cerevisiae and mammalian cells. The yeast pheromone response pathway has been adapted to allow ligand‐dependent signaling of heterologous expressed G‐protein coupled receptors (GPCRs) via mammalian or chimeric yeast/mammalian Gα proteins. Two different strategies are reported here which offer a positive screen for functional pairs. The OR and Gα protein are introduced into the modified yeast cells such that they hijack the pheromone response pathway usually resulting in cell cycle arrest. The first strategy utilizes ligand‐induced expression of a FUS1‐HIS3 reporter gene to permit growth on a selective medium lacking histidine; the second to induce ligand‐dependent expression of a FUS1‐Hph reporter gene, conferring resistance to hygromycin. Validation of the systems was performed using the rat I7 receptor response to a range of aldehyde odorants previously characterized as functional ligands. Of these only heptanal produced a positive growth response in the concentration range 5 × 10^?8 to 5 × 10^?6 M. Induction conditions appear to be critical for functional expression, and the solvents of odorants have a toxic effect for the highest odorant concentrations. The preference of rat I7 receptor for the ligand heptanal in yeast has to be compared to concurrent results obtained with mammalian expression systems.     

Yeasts as biological agents to control Botrytis cinerea

Yeasts, isolated from different sources, were identified and tested for inhibition using YMA-MB plates seeded with Botrytis cinerea strains. A total of 42 yeast strains of 20 different species were tested in vitro for antagonism against 18 pathogenic B. cinerea strains. Pichia membranifaciens, P. anomala and Debaryomyces hansenii displayed the most important inhibitory effect against Botrytis strains. In small-scale trials, post-harvest application of P. membranifaciens CYC 1106 to apple wounds inhibited B. cinerea CYC 20010. Purified killer toxin from P. membranifaciens CYC 1106 inhibited B. cinerea CYC 20010. Results indicated that certain yeasts, or their toxins such us P. membranifaciens CYC 1106 killer toxin, might have potential as novel agents to control B. cinerea.     

不同类型原油污染土壤生物修复技术研究

对不同类型原油污染土壤在实用规模的预制床上采用堆制技术进行生物修复 .通过投加肥料、菌剂、控制水分和pH ,可使微生物获得较好的生态环境 .当稀油、高凝油、特稠油和稠油污染的土壤中原油总量为 2 5 .8～ 77.2 g·kg-1土时 ,经过近 2个月的运行 ,石油总量的去除率可达 38.37%～ 5 6 .74 % .石油中芳烃、沥青和胶质混合物是制约石油快速降解的主要因素 .在处理过程中筛选出石油降解的优势菌株 ,其中有 6株真菌、6株细菌和 1株放线菌 .研究结果为石油污染土壤异位生物修复技术实用化提供了理论依据 .     

Lactic Acid Bacteria and Yeasts as Means of Decreasing Wine Acidity

Two hundred monocultures of lactic acid bacteria and 30 associations of yeasts and lactic acid bacteria have been studied. A stable association was developed which was capable of decreasing wine acidity. The association contained two species of bacteria, Leuconostoc oenosand Pediococcus pentosaceus, and the yeast Saccharomyces cerevisiae. The physiology of the microorganisms was studied, and their effects on the chemical composition of wines were determined.     

椰心叶甲的生物防治

椰心叶甲是近年来传入我国的危险性有害生物.1994年,我国内陆将椰心叶甲列为禁止入境的二类植物检疫危险性害虫.目前椰心叶甲在我国海南省、广东省、台湾省和香港地区危害严重并有蔓延趋势,严重危害了椰子、槟榔等棕榈科植物.针对椰心叶甲的危害特征,在实际防治应用中,化学防治,物理防治等方法不能起到很好的效果,生物防治是比较重要的防治方法.本文综述了对于椰心叶甲生物防治常用的几种防治方法:释放寄生蜂、病源微生物和生物农药等.椰心叶甲的生物学防治措施,关键是开发新的防治措施和提高现有方法的防治技术,达到持续有效控制.     

Fungi as Geologic Agents

Although many studies on fungi and geological processes have been published in recent years, books and congress proceedings on geomicrobiology focus mainly on prokaryotes and algae. Therefore, it is the aim of this review to summarize data on the fungal impact on geological processes. These processes include the alteration and weathering of rock and minerals, the accumulation of metals, and the conversion of fossil organic carbon. Fossil records and fungi in subsurface environments are also discussed. This article especially emphasizes the role of epi- and endolithic black meristematic fungi, discussing their deteriorative potential on rock as well as their taxonomy and phylogeny. Moreover, the impact of fungi on weathering of monuments and building materials is described and new methods to study fungi-material interactions are presented. The data summarized here show that "geomycology" is a highly interesting discipline in view of basic geological research, as well as biotechnological application.     

Potential Properties of Lactobacillus plantarum F-10 as a Bio-control Strategy for Wound Infections

In this study, Lactobacillus plantarum F-10, a promising probiotic strain isolated from fecal microbiota of healthy breastfed infant, was assessed as a bio-control strategy for wound infections. Pseudomonas aeruginosa PAO1/ATCC 27853, methicillin-resistant Staphylococcus aureus ATCC 43300, and their hospital-derived strains isolated from skin chronic wound samples were used as important skin pathogens. The cell-free extract (CFE) of the strain F-10 was shown to inhibit the growth of all pathogens tested, while no inhibition was observed when CFE was neutralized. The strain displayed no hemolysis and exhibited a strong auto-aggregating phenotype (51.48 ± 1.45%, 5 h) as well as co-aggregation. Antibiotic resistance profile was found to be safe according to the European Food Safety Authority. Biofilm formation was measured by crystal violet assay and visualized with scanning electron microscopy and confocal laser scanning microscopy. One hundred percent reduction in biofilm formation of all pathogens tested was obtained by sub-MIC value (12.5 mg/ml) of CFE following 24-h co-incubation. Inhibition of quorum sensing–controlled virulence factors (motility, protease and elastase activity, production of pyocyanin and rhamnolipid) of P. aeruginosa strains was also observed. DPPH radical scavenging activity of the CFE was determined as 88.57 ± 0.49%. In conclusion, our results suggest that L. plantarum F-10 may represent an alternative bio-control strategy against skin infections with its antimicrobial, anti-biofilm, anti-quorum sensing, and antioxidant activity.

     

Ketone Bodies as Anti-Seizure Agents

There is growing evidence that ketone bodies (KB)—derived from fatty acid oxidation and produced during fasting or consumption of high-fat diets—can exert broad neuroprotective effects. With respect to epilepsy, KB (such as β-hydroxybutyrate or BHB, acetoacetate and acetone) have been shown to block acutely induced and spontaneous recurrent seizures in various animal models. Although the mechanisms underlying the anti-seizure effects of KB have not been fully elucidated, recent experimental studies have invoked ketone-mediated effects on both inhibitory (e.g., GABAergic, purinergic and ATP-sensitive potassium channels) and excitatory (e.g., vesicular glutamate transporters) neurotransmission, as well as mitochondrial targets (e.g., respiratory chain and mitochondrial permeability transition). Moreover, BHB appears to exert both epigenetic (i.e., inhibition of histone deacetylases or HDACs) and anti-inflammatory (i.e., peripheral modulation of hydroxycarboxylic acid receptor and inhibition of the NOD-like receptor protein 3 or NRLP3 inflammasome) activity. While the latter two effects of BHB have yet to be directly linked to ictogenesis and/or epileptogenesis, parallel lines of evidence indicate that HDAC inhibition and a reduction in neuroinflammation alone or collectively can block seizure activity. Nevertheless, the notion that KB are themselves anti-seizure agents requires clinical validation, as prior studies have not revealed a clear correlation between blood ketone levels and seizure control. Notwithstanding this limitation, there is growing evidence that KB are more than just cellular fuels, and can exert profound biochemical, cellular and epigenetic changes favoring an overall attenuation in brain network excitability.     

Guanosine Analogues as Anti-Herpesvirus Agents

Abstract

Several guanosine analogues, i.e. acyclovir (and its oral prodrug valaciclovir), penciclovir (in its oral prodrug form, famciclovir) and ganciclovir, are widely used for the treatment of herpesvirus (i.e. HSV-1, HSV-2, VZV and HCMV) infections. In recent years, several new guanosine analogues have been developed, including the 3-membered (cyclopropyl) sugar derivative A-5021 and the 6-membered D- and L-cyclohexenyl derivatives. Prominent features shared by all guanosine analogues are the following. They depend for their phosphorylation on the virus-encoded thymidine kinase (TK), which makes them particularly effective against those viruses (HSV-1, HSV-2 and VZV) that encoded for such TK. They are also active against HCMV, whether or not they are subject of phosphorylation by the HCMV-induced UL97 protein kinase. Their antiviral activity can be markedly potentiated by mycophenolic acid, an IMP dehydrogenase inhibitor, and they hold great promise, not only as antiviral agents for the treatment of herpesvirus infections, but also as antitumor agents for the combined gene therapy/chemotherapy of cancer, provided that (part of) the tumor cells have been transfected by the viral TK gene.     

Chelating Agents as Histological and Histochemical Decalcifiers

The alterations caused by chelating agents (disodium ethylenediaminetetraacetate) used as decalcifying solutions at pH 7.0, in histological and histochemical technics have been studied comparatively. They have been controlled by the staining with hematoxylin and eosin, Gomori's aldehyde fuchsin, periodic acid-Schiff, metachromasia, and alkaline phosphatase. Their effect on the tissues was similar to that of buffered acid decalcifying solutions, such as that of Greep, Fischer and Morse (equal parts of 2% formic acid and 20% sodium citrate).

The use of 1% sodium diethylbarbiturate for 24 hr as a reactivating agent for alkaline phosphatase in the specimens treated with chelating agents is recommended.     

与细胞因子特异结合的寡聚核苷酸适配子及其在诊断和治疗中的应用

寡聚核苷酸适配子（Aptamer）是用指数富集式配基系统进化方法（SELEX）筛选出的寡聚核苷酸,它能与靶分子特异性结合,具有识别和抑制靶物质生物学活性的作用。将体外筛选到的寡聚核苷酸适配子作为在动物或人体内应用的药剂,还需要进行化学修饰来提高它的生物利用度和在血浆中的稳定性。2氟、2′烷氧基或2′氨基修饰可以提高适配子的稳定性,使适配子的体外半衰期延长;5′端交联一个高分子量的PEG分子或脂质体分子,可以使它的血浆清除率由1小时提高到几小时至1天。修饰后仍保持生物学活性的适配子可用于治疗相应靶细胞因子引起的疾病。目前,国内外已经筛选到了十几种细胞因子的适配子,其中血管内皮生长因子已经用于临床疾病的治疗。除了用于临床治疗外,适配子还可以用于细胞因子的诊断,凡是涉及抗体的诊断领域,几乎都可以用寡聚核苷酸适配子代替。应用大规模机械化筛选技术,可以在短期内筛选到大量的高特异性、高亲和力适配子,这将有力推动临床诊断和治疗的发展。     

Oligonucleotides and Derivatives as Gene-Specific Control Agents

Abstract

The current achievement of genome sequence projects of a dozen eukaryote organisms (including human genome) and the development of functional genomics are providing the basic knowledge required to utilize gene-specific reagents for both basic understanding of cell physiology and therapeutical development. The field of chemical genomics has the ambitious goal of designing molecules that could act selectively on every single gene or gene product in a cell and in vivo. The progress in oligonucleotide-based approaches will be the topic of this review, however, other nucleic acid- and SELEX-based approaches as well as high sequence-specific low molecular weight DNA-specific ligands will also be discussed.