Endophytic Trichoderma spp. can protect strawberry and privet plants from infection by the fungus Armillaria mellea

Armillaria mellea is an important fungal pathogen worldwide, affecting a large number of hosts in the horticulture and forestry industries. Controlling A. mellea infection is expensive, labour intensive and time-consuming, so a new, environmentally friendly management solution is required. To this effect, endophytic Trichoderma species were studied as a potential protective agent for Armillaria root rot (ARR) in strawberry and privet plants. A collection of forty endophytic Trichoderma isolates were inoculated into strawberry (Fragaria × ananassa) plants and plant growth was monitored for two months, during which time Trichoderma treatment had no apparent effect. Trichoderma-colonised strawberry plants were then inoculated with A. mellea and after three months plants were assessed for A. mellea infection. There was considerable variation in ARR disease levels between plants inoculated with different Trichoderma spp. isolates, but seven isolates reduced ARR below the level of positive controls. These isolates were further tested for protective potential in Trichoderma-colonized privet (Ligustrum vulgare) plants where five Trichoderma spp. isolates, including two highly effective Trichoderma atrobrunneum isolates, were able to significantly reduce levels of disease. This study highlights the potential of plants pre-colonised with T. atrobrunneum for effective protection against A. mellea in two hosts from different plant families

Structural characterization of toxic oligomers that are kinetically trapped during alpha-synuclein fibril formation

This is the author accepted manuscript. The final version is avialble via PNAS at http://www.pnas.org/content/112/16/E1994.long#ack-1.We describe the isolation and detailed structural characterization of stable toxic oligomers of α-synuclein that have accumulated during the process of amyloid formation. Our approach has allowed us to identify distinct subgroups of oligomers and to probe their molecular architectures by using cryo-electron microscopy (cryoEM) image reconstruction techniques. Although the oligomers exist in a range of sizes, with different extents and nature of β-sheet content and exposed hydrophobicity, they all possess a hollow cylindrical architecture with similarities to certain types of amyloid fibril, suggesting that the accumulation of at least some forms of amyloid oligomers is likely to be a consequence of very slow rates of rearrangement of their β-sheet structures. Our findings reveal the inherent multiplicity of the process of protein misfolding and the key role the β-sheet geometry acquired in the early stages of the self-assembly process plays in dictating the kinetic stability and the pathological nature of individual oligomeric species.We thank Dr. Katherine Stott, from the Biophysics Facility, Department of Biochemistry, University of Cambridge, for her assistance in using these facilities. This work was supported by the Agency for Science, Technology and Research, Singapore (S.W.C.), the “La Caixa” foundation (S.D.), Wellcome/MRC (Medical Research Council) Parkinson’s Disease Consortium Grant WT089698 (to E.D. and N.W.W.), National Institute for Health Research Biomedical Research Centres funding at University College London (to N.W.W.), the BBSRC through Grants BB/H003843/1 (to M.O.) and BB/E019927/1 (to C.M.D.), the Spanish Ministry of Economy and Competitiveness through Grants SAF 2012-39720 (to C.R.), BFU2013-44202 (to J.M.V.), and BIO2011-28941-C03-03 (to C.A. and G.R.), the Spanish Ministry of Health with cofunding by The European Regional Development Fund through Grant CP10/00527 (to C.R.), the Madrid Regional Government through Grant S2013/MIT-2807 (to J.M.V.), Parkinson’s UK through Grant H-0903 (to T.G.), the Wellcome Trust, the Leverhulme Trust, the European Commission through project LSHM-CT-2006-037525 (to C.M.D.), the Medical Research Council through Grant MRC G1002272 (to E.J.D.-G. and C.M.D.), and the Engineering and Physical Sciences Research Council (C.M.D.). A.Y.A. was a Parkinson’s UK Senior Research Fellow. N.C. is a Royal Society Research Fellow and also acknowledges financial support by the Human Frontier Science Program from Long-Term Fellowship LT000795/2009

New Mediterranean Biodiversity Records (April 2015)

The Collective Article ‘New Mediterranean Biodiversity Records’ of the Mediterranean Marine Science journal offers the means to publish biodiversity records in the Mediterranean Sea. The current article is divided in two parts, for records of native and alien species respectively. The new records of native fish species include: the slender sunfish Ranzania laevis and the scalloped ribbonfish Zu cristatus in Calabria; the Azores rockling Gaidropsarus granti in Calabria and Sicily; the agujon needlefish Tylosu¬rus acus imperialis in the Northern Aegean; and the amphibious behaviour of Gouania willdenowi in Southern Turkey. As regards molluscs, the interesting findings include Ischnochiton usticensis in Calabria and Thordisa filix in the bay of Piran (Slovenia). The stomatopod Parasquilla ferussaci was collected from Lesvos island (Greece); the isopod Anilocra frontalis was observed parasit¬izing the alien Pteragogus trispilus in the Rhodes area. The asteroid Tethyaster subinermis and the butterfly ray Gymnura altavela were reported from several localities in the Greek Ionian and Aegean Seas.The new records of alien species include: the antenna codlet Bregmaceros atlanticus in Saronikos Gulf; three new fish records and two decapods from Egypt; the establishment of the two spot cardinal fish Cheilodipterus novemstriatus and the first record of the marble shrimp Saron marmoratus in semi-dark caves along the Lebanese coastline; the finding of Lagocephalus sceleratus, Sargocentron rubrum, Fistularia commersonii and Stephanolepis diaspros around Lipsi island (Aegean Sea, Greece); the decapod Penaeus Hathor in Aegean waters; the decapod Penaeus aztecus and the nudibranch Melibe viridis in the Dodecanese islands; the finding of Pinctada imbricata radiate in the Mar Grande of Taranto (Ionian Sea, Italy) and the Maliakos Gulf (Greece)

Effect of Virulence Factors on the Photodynamic Inactivation of Cryptococcus neoformans

Opportunistic fungal pathogens may cause an array of superficial infections or serious invasive infections, especially in immunocompromised patients. Cryptococcus neoformans is a pathogen causing cryptococcosis in HIV/AIDS patients, but treatment is limited due to the relative lack of potent antifungal agents. Photodynamic inactivation (PDI) uses the combination of non-toxic dyes called photosensitizers and harmless visible light, which produces singlet oxygen and other reactive oxygen species that produce cell inactivation and death. We report the use of five structurally unrelated photosensitizers (methylene blue, Rose Bengal, selenium derivative of a Nile blue dye, a cationic fullerene and a conjugate between poly-L-lysine and chlorin(e6)) combined with appropriate wavelengths of light to inactivate C. neoformans. Mutants lacking capsule and laccase, and culture conditions that favoured melanin production were used to probe the mechanisms of PDI and the effect of virulence factors. The presence of cell wall, laccase and melanin tended to protect against PDI, but the choice of the appropriate photosensitizers and dosimetry was able to overcome this resistance.Fundação de Amparo à Pesquisa do Estado de São Paulo (2010/13313–9

Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae

[abridged] Background: The distribution of chemical species in an open system at metastable equilibrium can be expressed as a function of environmental variables which can include temperature, oxidation-reduction potential and others. Calculations of metastable equilibrium for various model systems were used to characterize chemical transformations among proteins and groups of proteins found in different compartments of yeast cells. Results: With increasing oxygen fugacity, the relative metastability fields of model proteins for major subcellular compartments go as mitochondrion, endoplasmic reticulum, cytoplasm, nucleus. In a metastable equilibrium setting at relatively high oxygen fugacity, proteins making up actin are predominant, but those constituting the microtubule occur with a low chemical activity. A reaction sequence involving the microtubule and spindle pole proteins was predicted by combining the known intercompartmental interactions with a hypothetical program of oxygen fugacity changes in the local environment. In further calculations, the most-abundant proteins within compartments generally occur in relative abundances that only weakly correspond to a metastable equilibrium distribution. However, physiological populations of proteins that form complexes often show an overall positive or negative correlation with the relative abundances of proteins in metastable assemblages. Conclusions: This study explored the outlines of a thermodynamic description of chemical transformations among interacting proteins in yeast cells. The results suggest that these methods can be used to measure the degree of departure of a natural biochemical process or population from a local minimum in Gibbs energy.Comment: 32 pages, 7 figures; supporting information is available at http://www.chnosz.net/yeas

Degradation attacks on Passive Optical Networks

Passive Optical Networks (PONs) are a promising candidate to solve the last-mile problem in access networks. By using optical fibers, PONs can offer to the subscribers higher capacity than other traditional access technologies, such as xDSL or Cable-TV, at a lower cost than FTTx solutions. As for any other access-network technology, security is a very important issue. PONs have very specific security requirements because (i) the downstream transmission channel is inherently broadcast, and (ii) malicious transmissions in the upstream channel can not be easily detected and prevented. This paper shows that malicious upstream transmissions can be used to conduct very intrusive degradation attacks upon the upstream traffic and quantifies the decrement of the upstream throughput over a PON under different scenarios of degradation attack. Further, the paper considers how the effect of a degradation attack carried on at the physical layer is greatly amplified by the TCP congestion control algorithm resulting in a strong degradation with little effort by the attacker. The attacker could then exploit bandwidth sharing mechanisms to gain an unfair amount of bandwidth. We also propose a possible mitigation strategy that pinpoints the attacker and re-establishes fairness in terms of throughput per ONU

Competition Law in Kosovo: Problems and Challenges

Competition Law is an important aspect of free market economy. It determines the functioning of the economic system based on the free market principles of supply and demand. Competition law is in the initial stage of its implementation in the Republic of Kosovo. Its development began in 2004 with the adoption of Kosovo’s Law on Competition, the country’s very first law passed to regulate the legal basis of free market competition. The Law on Competition of 2004 had many shortcomings both with respect to its content and implementation. New legislation was thus passed in 2010 under the name the Law on the Protection of Competition. The latter act is in force now along with an Amendment that entered into force in early 2014. Taken in its entirety, Kosovo’s competition law meets the standards and is in accordance with EU legislation. Kosovo, although it is only in the initial stage of its contractual relations with the EU, has aligned most of its laws with the requirements of EU legislation. Kosovo is Europe’s youngest country and as such, it has various problems when it comes to the functioning of the rule of law. This paper will discuss several topics related to the development of competition law in Kosovo including: the political, legal and economical situation in the field of competition law; the legal bases for the protection of competition in Kosovo; the Kosovo Competition Authority and the insufficiency in its capacities to combat competition law infringements; legal provisions on restrictive practices and merger control. The paper also includes comprehensive conclusions. A number of competition cases deal with by the Kosovo Competition Authority will be mentioned throughout the paper

The crystal structure of human XPG, the xeroderma pigmentosum group G endonuclease, provides insight into nucleotide excision DNA repair

16 p.-7 fig.-1 tab.Nucleotide excision repair (NER) is an essential pathway to remove bulky lesions affecting one strand of DNA. Defects in components of this repair system are at the ground of genetic diseases such as xeroderma pigmentosum (XP) and Cockayne syndrome (CS). The XP complementation group G (XPG) endonuclease cleaves the damaged DNA strand on the 3' side of the lesion coordinated with DNA re-synthesis. Here, we determined crystal structures of the XPG nuclease domain in the absence and presence of DNA. The overall fold exhibits similarities to other flap endonucleases but XPG harbors a dynamic helical arch that is uniquely oriented and defines a gateway. DNA binding through a helix-2-turn-helix motif, assisted by one flanking alpha-helix on each side, shows high plasticity, which is likely relevant for DNA scanning. A positively-charged canyon defined by the hydrophobic wedge and beta-pin motifs provides an additional DNA-binding surface. Mutational analysis identifies helical arch residues that play critical roles in XPG function. A model for XPG participation in NER is proposed. Our structures and biochemical data represent a valuable tool to understand the atomic ground of XP and CS, and constitute a starting point for potential therapeutic applications.Spanish Ministry of Science [BFU2017-87397-P,BFU2013-48374-P to C.F.T.]; PharmaMar partly funded this project. Funding for open access charge: The CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI)Peer reviewe