Timing of breeding and diet of the Black-faced cormorant Phalacrocorax fuscescens

Previous anecdotal reports have suggested that Black-faced Cormorant Phalacrocorax fuscescens breeds only in winter in southeastern Australia, but detailed reports confirming this are lacking. Here we examine the timing of breeding in Black-faced Cormorants at Notch Island in northern Bass Strait in 2006. Peak laying occurred during winter (ca 26 July). The diet of Black-faced Cormorants was predominantly fish (97% of identified prey) and varied between breeding and post-breeding periods. Black-faced Cormorants consumed a total of 14 different species with four species having a frequency of occurrence in the diet of ?5% during the breeding season and six species during the post-breeding period. We provide data for the first time on the chronology of breeding of Black-faced Cormorants in one year and give a preliminary description of their diet based on pellet analyses. We propose that late winter breeding may be a strategy to avoid the high ambient temperatures in northern Bass Strait during summer, the associated higher thermoregulatory costs for adults and the increased mortality for chicks

From orphan phage to a proposed new family–the diversity of N4-like viruses

Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. In recent years, due to new and relatively inexpensive sequencing techniques the number of publicly available phage genome sequences expanded rapidly. This revealed new members of the N4-like phage group, from 33 members in 2015 to 115 N4-like viruses in 2020. Using new technologies and methods for classification, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has moved the classification and taxonomy of bacterial viruses from mere morphological approaches to genomic and proteomic methods. The analysis of 115 N4-like genomes resulted in a huge reassessment of this group and the proposal of a new family “Schitoviridae”, including eight subfamilies and numerous new genera

Genome sequence of vB_AbaS_TRS1, a viable prophage isolated from Acinetobacter baumannii strain A118

© 2016 Turner et al. A novel temperate phage, vB_AbaS_TRS1, was isolated from cultures of Acinetobacter baumannii strain A118 that had been exposed to mitomycin C. Phage TRS1 belongs to the Siphoviridae family of bacteriophages and encapsulates a 40,749-bp genome encoding 70 coding sequences and a single tRNA

A roadmap for genome-based phage taxonomy

Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy

Comparative analysis of 37 Acinetobacter bacteriophages

© 2017 by the authors. Licensee MDPI, Basel, Switzerland. Members of the genus Acinetobacter are ubiquitous in the environment and the multipledrug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades

Short-chain lipid peroxidation products form covalent adducts with pyruvate kinase and inhibit its activity in vitro and in breast cancer cells

Pyruvate kinase catalyses the last step in glycolysis and has been suggested to contribute to the regulation of aerobic glycolysis in cancer cells. It can be inhibited by oxidation of cysteine residues in vitro and in vivo, which is relevant to the more pro-oxidant state in cancer and proliferating tissues. These conditions also favour lipid peroxidation and the formation of electrophilic fragmentation products, including short-chain aldehydes that can covalently modify proteins. However, as yet few studies have investigated their interactions with pyruvate kinase, so we investigated the effects of three different aldehydes, acrolein, malondialdehyde and 4-hydroxy-2(E)-hexenal (HHE), on the structure and activity of the enzyme. Analysis by LC-MS/MS showed unique modification profiles for each aldehyde, but Cys152, Cys423 and Cys474 were the residues most susceptible to electrophilic modification. Analysis of enzymatic activity under these conditions showed that acrolein was the strongest inhibitor, and at incubation times longer than 2 h, pathophysiological concentrations induced significant effects. Treatment of MCF-7 cells with the aldehydes caused similar losses of pyruvate kinase activity to those observed in vitro, and at lower concentrations than those required to cause cell death, with time and dose-dependent effects; acrolein adducts on Cys152 and Cys358 were detected. Cys358 and Cys474 are located at or near the allosteric or active sites, and formation of adducts on these residues probably contributes to loss of activity at low treatment concentrations. This study provides the first detailed analysis of the structure-activity relationship of C3 and C6 aldehydes with pyruvate kinase, and suggests that reactive short-chain aldehydes generated in diseases with an oxidative aetiology or from environmental exposure such as smoking could be involved in the metabolic alterations observed in cancer cells, through alteration of pyruvate kinase activity

The Human Kernel

Bayesian nonparametric models, such as Gaussian processes, provide a compelling framework for automatic statistical modelling: these models have a high degree of flexibility, and automatically calibrated complexity. However, automating human expertise remains elusive; for example, Gaussian processes with standard kernels struggle on function extrapolation problems that are trivial for human learners. In this paper, we create function extrapolation problems and acquire human responses, and then design a kernel learning framework to reverse engineer the inductive biases of human learners across a set of behavioral experiments. We use the learned kernels to gain psychological insights and to extrapolate in human-like ways that go beyond traditional stationary and polynomial kernels. Finally, we investigate Occam's razor in human and Gaussian process based function learning.Comment: 11 pages, 5 figures. To appear in Neural Information Processing Systems (NIPS) 2015. Version 2: Figure 2 (i)-(n) now displays the second set of progressive function learning experiment