Contamination effects by a ‘conventional’ and a ‘biodegradable’ lubricant oil on infaunal recruitment to Antarctic sediments: A field experiment

To investigate the impacts of synthetic lubricants on Antarctic infaunal communities, a field experiment was setup near Australia's Casey Station, East Antarctica. Two types of synthetic lubricants were tested: an ‘Unused’ and ‘Used’ conventional synthetic lubricant, and an alternative marketed as ‘biodegradable’. Clean defaunated sediment was contaminated with the lubricants, decanted into trays, and deployed by divers onto the seabed in a randomised block design. Sediments were sampled 5 and 56 weeks after deployment. After 5 weeks, benthic assemblages that had recruited to the lubricant contaminated sediments were significantly different to those in ‘Control’ sediments, and differences were more pronounced after 56 weeks. Total number of individuals did not significantly differ between treatments after 5 weeks. However, after 56 weeks total individuals in the ‘Control’ sediments were significantly greater than in the contaminated sediments. Nototanais antarcticus (tanaid) and to a lesser extent Monoculodes sp. (gammarid), Tanaid sp. IV and Eudorella sp. (cumacean) had significantly higher abundances in the control sediments after 56 weeks compared to the contaminated sediments. Copepods numerically dominated the benthic assemblages at both sampling times; however, their abundance did not significantly differ across treatments. The community recruiting to the contaminated sediments remained different from that in the ‘Control’ sediments for the duration of the experiment (1 year). The ‘biodegradable’ lubricant was just as environmentally harmful to the Antarctic infauna as the ‘conventional’ lubricant currently used at Australia's Antarctic stations. Our results demonstrate that changes to recruitment are one of the potential environmental consequences of a lubricant spill to Antarctic benthic communities, and reinforce the importance of preventative oil spill management and effective clean-up procedures. Further monitoring of this field experiment will provide much needed information about the long-term impacts by synthetic lubricants in the Antarctic marine environment.     

The pCLEAN dual binary vector system for Agrobacterium-mediated plant transformation

The development of novel transformation vectors is essential to the improvement of plant transformation technologies. Here, we report the construction and testing of a new multifunctional dual binary vector system, pCLEAN, for Agrobacterium-mediated plant transformation. The pCLEAN vectors are based on the widely used pGreen/pSoup system and the pCLEAN-G/pCLEAN-S plasmids are fully compatible with the existing pGreen/pSoup vectors. A single Agrobacterium can harbor (1) pCLEAN-G and pSoup, (2) pGreen and pCLEAN-S, or (3) pCLEAN-G and pCLEAN-S vector combination. pCLEAN vectors have been designed to enable the delivery of multiple transgenes from distinct T-DNAs and/or vector backbone sequences while minimizing the insertion of superfluous DNA sequences into the plant nuclear genome as well as facilitating the production of marker-free plants. pCLEAN vectors contain a minimal T-DNA (102 nucleotides) consisting of direct border repeats surrounding a 52-nucleotide-long multiple cloning site, an optimized left-border sequence, a double left-border sequence, restriction sites outside the borders, and two independent T-DNAs. In addition, selectable and/or reporter genes have been inserted into the vector backbone sequence to allow either the counter-screening of backbone transfer or its exploitation for the production of marker-free plants. The efficiency of the different pCLEAN vectors has been assessed using transient and stable transformation assays in Nicotiana benthamiana and/or Oryza sativa.     

The cell cycle hypothesis of Alzheimer's disease: suggestions for drug development

The cell cycle of hypothesis of neural dysfunction in chronic neurodegenerative conditions such as Alzheimer's disease (AD) offers a unified approach to understanding both existing and novel strategies for drug development. At the present time, a ligand based approach is a pragmatic solution for identifying new chemical leads on which to base future discovery and optimisation. We have pursued a ligand based approach on the basis of public domain data to identify existing compounds capable of abrogating the cell cycle at the G0-G1 interface. Selected on this basis, irrespective of the tissue under study, we identified several classes of compounds as potential chemical leads. Of these compounds, at least ten have already been shown to be neuroprotective in animal models of acute neurodegeneration. Such compounds could form the basis of a screening exercise after development of suitable screening tools. Progressing of chemical leads through such an approach will be more efficient if future leads display relevant "drug-like" properties. Further, drug development in this arena should take account of the special concerns raised by targeting an elderly population. This will involve accounting for frequent polypharmacy in the aging population, and age-related alterations in physiology.     

Retracted: A new species in town: New record of Hexanchus nakamurai Teng, 1962 from the Levantine Sea

Hexanchus nakamurai is a deep-water species, with very little scientific information. This study confirms the distribution of the species in the most eastern region of the Mediterranean Sea, Levantine Sea, in addition to providing some biological information from four pregnant individuals, which is being reported for the first time in the Mediterranean Sea. A total of four individuals were bycaught, in two sets on opposite coasts, three on the 13th of May 2020 from the western coast, and an individual on the 14th June 2020 from east coast of the island of Cyprus. The four specimens, all pregnant females, measured between 107 and 116 cm in total length and between 4,330 and 4,960 g in weight. All specimens were in early pregnancy according to the level of embryo development, which confirms that the size at maturity is smaller than previously reported. In the stomachs, remains of the hake Merluccius merluccius, the cephalopod Loligo vulgaris and two unidentified species of Hirudinea (Annelida) were found. This study provides important new information on the Mediterranean distribution of a globally rare and data deficient species, including an expansion of its known range, dietary preferences and insights of its reproduction biology; the first pregnant females reported in the Mediterranean Sea.     

Yeast Endocytic Adaptor AP‐2 Binds the Stress Sensor Mid2 and Functions in Polarized Cell Responses

The AP‐2 complex is a heterotetrameric endocytic cargo‐binding adaptor that facilitates uptake of membrane proteins during mammalian clathrin‐mediated endocytosis. While budding yeast has clear homologues of all four AP‐2 subunits which form a complex and localize to endocytic sites in vivo, the function of yeast AP‐2 has remained enigmatic. Here, we demonstrate that AP‐2 is required for hyphal growth in Candida albicans and polarized cell responses in Saccharomyces cerevisiae. Deletion of APM4, the cargo‐binding mu subunit of AP‐2, causes defects in pseudohyphal growth, generation of a mating projection and the cell wall damage response. In an apm4 null mutant, the cell wall stress sensor Mid2 is unable to relocalize to the tip of a mating projection following pheromone addition, or to the mother bud neck in response to cell wall damage. A direct binding interaction between Mid2 and the mu homology domain of Apm4 further supports a model in which AP‐2 binds Mid2 to facilitate its internalization and relocalization in response to specific signals. Thus, Mid2 is the first cargo for AP‐2 identified in yeast. We propose that endocytic recycling of Mid2 and other components is required for polarized cell responses ensuring cell wall deposition and is tightly monitored during cell growth.      

FRASS: the web-server for RNA structural comparison

Background  

The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules.     

Improving the quality of protein structure models by selecting from alignment alternatives

Background  

In the area of protein structure prediction, recently a lot of effort has gone into the development of Model Quality Assessment Programs (MQAPs). MQAPs distinguish high quality protein structure models from inferior models. Here, we propose a new method to use an MQAP to improve the quality of models. With a given target sequence and template structure, we construct a number of different alignments and corresponding models for the sequence. The quality of these models is scored with an MQAP and used to choose the most promising model. An SVM-based selection scheme is suggested for combining MQAP partial potentials, in order to optimize for improved model selection.     

Subcellular localization of recently-absorbed iron in mouse duodenal enterocytes: identification of a basolateral membrane iron-binding site

The subcellular distribution of newly absorbed iron in isolated mouse duodenal enterocytes was investigated by analytical subcellular fractionation using sucrose density gradient centifugation. Two major peaks of mucosal 59Fe activity were observed: one soluble and one particulate (density 1.18-1.20 g ml-1). The latter was increased following prior exposure of animals to chronic hypoxia. The particulate 59Fe was localized to the basolateral membranes using the marker enzyme Na+, K+ activated, Mg2+ dependent, ATPase and by washing intact enterocytes with the selective plasma membrane perturbant digitonin. The basolateral membrane can be selectively labelled by in vitro incubation of intact enterocytes at 0 degrees C with 59Fe(III)-nitrilotriacetate complex, confirming the presence of a 59Fe binding site on this membrane. No significant difference in in vitro iron binding to this site was observed between normal and chronically hypoxic animals. Iron binding to the basolateral membrane was significantly higher in disrupted, compared to intact enterocytes, indicating that this site is present on both sides of the basolateral membrane. It is therefore suggested that the increased labelling of this site in hypoxia, in vivo, is a consequence of an increase in a mucosal Fe pool which is available for binding to a membrane receptor.