Cylindrocarpon root rot: multi-gene analysis reveals novel species within the Ilyonectria radicicola species complex

Ilyonectria radicicola and its Cylindrocarpon-like anamorph represent a species complex that is commonly associated with root rot disease symptoms on a range of hosts. During the course of this study, several species could be distinguished from I. radicicola sensu stricto based on morphological and culture characteristics. DNA sequence analysis of the partial ??-tubulin, histone H3, translation elongation factor 1-?? and nuclear ribosomal RNA-Internal Transcribed Spacer (nrRNA-ITS) genes were employed to provide further support for the morphological species resolved among 68 isolates associated with root rot disease symptoms. Of the various loci screened, nrRNA-ITS sequences were the least informative, while histone H3 sequences were the most informative, resolving the same number of species as the combined dataset across the four genes. Within the Ilyonectria radicicola species complex, 12 new taxa are delineated occurring on a diverse range of hosts, the most common being Cyclamen, Lilium, Panax, Pseudotsuga, Quercus and Vitis.     

Targeted therapy for LIMD1-deficient non-small cell lung cancer subtypes

An early event in lung oncogenesis is loss of the tumour suppressor gene LIMD1 (LIM domains containing 1); this encodes a scaffold protein, which suppresses tumorigenesis via a number of different mechanisms. Approximately 45% of non-small cell lung cancers (NSCLC) are deficient in LIMD1, yet this subtype of NSCLC has been overlooked in preclinical and clinical investigations. Defining therapeutic targets in these LIMD1 loss-of-function patients is difficult due to a lack of ‘druggable’ targets, thus alternative approaches are required. To this end, we performed the first drug repurposing screen to identify compounds that confer synthetic lethality with LIMD1 loss in NSCLC cells. PF-477736 was shown to selectively target LIMD1-deficient cells in vitro through inhibition of multiple kinases, inducing cell death via apoptosis. Furthermore, PF-477736 was effective in treating LIMD1^−/− tumours in subcutaneous xenograft models, with no significant effect in LIMD1^+/+ cells. We have identified a novel drug tool with significant preclinical characterisation that serves as an excellent candidate to explore and define LIMD1-deficient cancers as a new therapeutic subgroup of critical unmet need.Subject terms: Targeted therapies, Non-small-cell lung cancer     

Identification of novel phospholipid binding proteins in Saccharomyces cerevisiae

A proteomics approach was used to search for novel phospholipid binding proteins in Saccharomyces cerevisiae. Phospholipids were immobilized on a solid support and the lipids were probed with soluble yeast protein extracts. From this, the phosphatidic acid binding proteins were eluted and identified by mass spectrometry. Thirteen proteins were identified and 11 of these were previously unknown lipid binding proteins. The protein-lipid interactions identified would not have been predicted using bioinformatics approaches as none possessed a known lipid binding motif. A subset of the identified proteins was purified to homogeneity and determined to directly bind phospholipids immobilized on a solid support or organized into liposomes. This simple approach could be systematically applied to perform an exhaustive screen for soluble lipid binding proteins in S. cerevisiae or other organisms.     

Regional differences in foraging behaviour of invasive green crab (<Emphasis Type=Italic>Carcinus maenas</Emphasis>) populations in Atlantic Canada

Invasive green crab populations initially established in Canada within the Bay of Fundy, New Brunswick in the 1950s and were present in all five Atlantic provinces by 2007. Genetic evidence suggests that the Atlantic Canadian populations originated from two separate introductions with differences in time of establishment among regions and possible population-level behavioural differences. In this study, we examine intraspecific foraging behaviour among crabs from different populations, and interspecific foraging behaviour between genetically similar crabs and juvenile lobsters. Both sets of foraging experiments involved competition for a limited food source over a 1-h period. In intraspecific match-ups, recent invaders from Newfoundland (NL) were significantly superior foragers than long-established invaders from Nova Scotia (NS) and New Brunswick (NB) populations; however, we found no differences between NL and Prince Edward Island (PE) invaders. Crabs from PE were better competitors than those from NS and NB, but these differences were not significant. Interspecific competition experiments indicated that the feeding behaviour of recent invaders (NL) and genetically similar, but long-established invaders (NS), differed in the presence of juvenile lobsters. Our study documents striking behavioural differences among populations of green crab from a small geographic region, which may reflect a combination of both genetic differences and time since establishment. These differences may result in varying impacts on newly invaded habitats.     

Community-based processes behind species richness gradients: contrasting abundance–extinction dynamics and sampling effects in areas of low and high productivity

Aim  To consider the role of local colonization and extinction rates in explaining the generation and maintenance of species richness gradients at the regional scale.
Location  A Mediterranean biome (oak forests, deciduous forests, shrublands, pinewoods, firwoods, alpine heathlands, crops) in Catalonia, Spain.
Methods  We analysed the relative importance of direct and indirect effects of community size in explaining species richness gradients. Direct sampling effects of community size on species richness are predicted by Hubbell's neutral theory of biodiversity and biogeography. The greater the number of individuals in a locality, the greater the number of species expected by random direct sampling effects. Indirect effects are predicted by the abundance–extinction hypothesis, which states that in more productive sites increased population densities and reduced extinction rates may lead to high species richness. The study system was an altitudinal gradient of forest bird species richness.
Results  We found significant support for the existence of both direct and indirect effects of community size in species richness. Thus, both the neutral and the abundance–extinction hypotheses were supported for the altitudinal species richness gradient of forest birds in Catalonia. However, these mechanisms seem to drive variation in species richness only in low-productivity areas; in high-productivity areas, species richness was uncorrelated with community size and productivity measures.
Main conclusions  Our results support the existence of a geographical mosaic of community-based processes behind species richness gradients, with contrasting abundance–extinction dynamics and sampling effects in areas of low and high productivity.     

Effects of adults body size and larvae diet on the fecundity and percent fertility of eggs laid by Xylotrechus arvicola (Coleoptera: Cerambycidae) females,insect pest in Spanish vineyards

Xylotrechus arvicola is a pest of grape in some vine‐producing regions of the Iberian Peninsula. Biological parameters and relationships (fecundity and percent fertility of eggs in relationship to body size) of females obtained in the laboratory and captured in vineyards were studied. In laboratory conditions, the mean developmental time of larvae ranged from 384 to 392 days and pupal stage varied between 12 to 14 days. Body size (BS) of X. arvicola females was significantly bigger than males. Fecundity was greater in the laboratory (147 eggs) than in the field (50 eggs) females, but the percent fertility of the laboratory eggs was lower (16 eggs). Laboratory females showed a bigger relationship between the production of eggs and BS than females captured in vineyards. Wild females (PDO Ribera del Duero and Tierra de León) had a positive relationship between the percent fertility of eggs and the BS. No correlation between the percent fertility of eggs and the BS was displayed by females captured in PDO Toro, but these females had a higher percent fertility (53 eggs) than the others PDO's. These biological parameters and relationships studied suggest that the artificial diet may lack certain essential nutrients that vine varieties can provide that favor the fertility of eggs. This explains why wild females have the potential to become a problem pest in the Tempranillo grape variety, with bilateral cordon and bush vines training systems that have the highest incidence of this cerambycid.     

Piezoelectric biosensors for biorecognition analysis: application to the kinetic study of HIV-1 Vif protein binding to recombinant antibodies

In this work three piezoelectric sensors modified with anti-HIV-1 Vif (virion infectivity factor) single fragment antibodies (4BL scFV), single domains (VH) and camelized single domains (VHD) were constructed and used to detect HIV1 Vif in liquid samples. Dithio-bis-succinimidyl-undecanoate (DSU) and 11-hydroxy-1-undecanethiol (HUT) mixed self assembled monolayers (SAM) were generated at the sensors surface onto which the antibodies were immobilized. All sensors detected specifically the target HIV1-Vif antigen in solution and no unspecific binding was monitored. Impedance analysis was performed to quantify electroacoustic and viscoelastic interferences during antibody immobilization and antigen recognition. The elimination of such interferences enabled the quantitative use of the piezoelectric immunosensors to estimate the antibody surface density as well as antigen binding and equilibrium constants. In spite of the possible limitation regarding mass transport and other related molecular phenomena, which were not considered in the binding model used, this work demonstrates the usefulness of piezoelectric biosensors in biorecognition analysis and evidences the advantages on using simultaneous impedance analysis to bring analytical significance to measured data, and thus to improve piezoelectric sensors sensitivity and applicability.     

Combined Microbial-Fe(0) Treatment System to Remove Nitrate from Contaminated Groundwater

Experiments were conducted to delineate the applicability and limitations of biologically active Fe(0) barriers to remove nitrate under various geochemical and hydraulic conditions. Microcosm studies showed that, while no Fe(0) treatment was needed to remove nitrate from a high-carbon soil, adding Fe(0) to a low-carbon soil supplemented the electron donor pool and enhanced nitrate removal. Montmorillonite, an acidic aluminosilicate mineral, enhanced Fe(0) corrosion and nitrate removal (from about 1 to 3 mg/L NO₃-N per day), and reduced the transient accumulation of nitrite. Combining autotrophic denitrifiers (e.g., Paracoccus denitrificans) with Fe(0) significantly reduced the amount of nitrite eluted from aquifer columns, from up to 7 to less than 1 mg/L NO₂∼-N. Bacteria were observed to preferentially colonize the Fe(0) surface, which produces cathodic H₂ when corroded by water. The preferential colonization of Fe(0) suggests that hydrogenotrophic consortia are likely to develop around Fe(0) walls to exploit cathodic depolarization as a metabolic niche.