Another Really, Really Big Virus

Viruses with genomes larger than 300 kb and up to 1.2 Mb, which encode hundreds of proteins, are being discovered and characterized with increasing frequency. Most, but not all, of these large viruses (often referred to as giruses) infect protists that live in aqueous environments. Bioinformatic analyses of metagenomes of aqueous samples indicate that large DNA viruses are quite common in nature and await discovery. One issue that is perhaps not appreciated by the virology community is that large viruses, even those classified in the same family, can differ significantly in morphology, lifestyle, and gene complement. This brief commentary, which will mention some of these unique properties, was stimulated by the characterization of the newest member of this club, virus CroV (Fischer, M.G.; Allen, M.J.; Wilson, W.H.; Suttle, C.A. Giant virus with a remarkable complement of genes infects marine zooplankton. Proc. Natl. Acad. Sci. USA 2010, 107, 19508–19513 [1]). CroV has a 730 kb genome (with ∼544 protein-encoding genes) and infects the marine microzooplankton Cafeteria roenbergensis producing a lytic infection

Modelling rankings in R: the PlackettLuce package

This paper presents the R package PlackettLuce, which implements a generalization of the Plackett-Luce model for rankings data. The generalization accommodates both ties (of arbitrary order) and partial rankings (complete rankings of subsets of items). By default, the implementation adds a set of pseudo-comparisons with a hypothetical item, ensuring that the underlying network of wins and losses between items is always strongly connected. In this way, the worth of each item always has a finite maximum likelihood estimate, with finite standard error. The use of pseudo-comparisons also has a regularization effect, shrinking the estimated parameters towards equal item worth. In addition to standard methods for model summary, PlackettLuce provides a method to compute quasi standard errors for the item parameters. This provides the basis for comparison intervals that do not change with the choice of identifiability constraint placed on the item parameters. Finally, the package provides a method for model-based partitioning using covariates whose values vary between rankings, enabling the identification of subgroups of judges or settings that have different item worths. The features of the package are demonstrated through application to classic and novel data sets.Comment: In v2: review of software implementing alternative models to Plackett-Luce; comparison of algorithms provided by the PlackettLuce package; further examples of rankings where the underlying win-loss network is not strongly connected. In addition, general editing to improve organisation and clarity. In v3: corrected headings Table 4, minor edit

Ring resonator-based Tunable Optical Delay Line in LPCVD Waveguide Technology

Optical circuits providing a time delay to signals modulated on optical carriers are considered important for optical communication systems and phased array antennas. A continuously tunable optical delay line is demonstrated in low-cost CMOS compatible LPCVD planar waveguide technology. The device consists of three cascaded ringresonator all-pass filters with fixed circumference of 2 cm (delay of 0.12 ns and FSR of 8.4 GHz). The measured group delay ranges from 0 ns up to 1.2 ns with a bandwidth of 500 MHz and delay ripple smaller than 1 ps, which is in accordance with the calculations

PROMOTERS FROM CHLORELLAVIRUS GENES PROVIDING EXPRESSION OF GENES IN PROKARYOTIC AND EUKARYOTIC HOSTS

The invention is directed to novel promoters or mutants thereof from Chlorella virus DNA methyltransferase genes. A Chlorella virus gene promoter is operably linked to a first and/or second DNA sequence encoding a gene that is different from the Chlorella virus gene to form an expression cassette. An expression cassette can be introduced into prokaryotic and/or eukaryotic cells and can provide for a high level of expression of the gene encoded by the first and/or second DNA sequence. The invention also provides a method for screening other Chlorella virus genes for promoters that can function to express a heterologous gene in prokaryotic and/or eukaryotic hosts

Synthesis and Localization of a Development-Specific Protein in Sclerotia of \u3ci\u3eSclerotinia sclerotiorum\u3c/i\u3e

A development-specific protein (SSP) makes up about 35 to 40% of the total protein in sclerotia of the fungus Sclerotinia sclerotiorum. The protein consists of three charge isomers, with one isomer making up 80 to 90% of the total. In vitro translation of poly(A)+ RNA isolated from cells in early stages of sclerotia formation revealed that 44% of the amino acids incorporated was into SSP. In vivo- and in vitro-synthesized forms of SSP migrated at identical rates on both isoelectric focusing and denaturing polyacrylamide gels, indicating that SSP was not synthesized as a larger precursor. This was significant because SSP accumulated in membrane-bound, organellelike structures which resemble protein bodies found in seeds of many higher plants

PROMOTERS FROM CHLORELLA VIRUS GENES PROVIDING FOR EXPRESSION OF GENES IN PROKARYOTIC AND EUKARYOTIC HOSTS

The invention is directed to novel promoters or mutants thereof from Chlorella virus DNA methyltansferase genes. A Chlorella Virus gene promoter is operably linked to a first and/or Second DNA sequence encoding a gene that is different from the Chlorella virus to form an expression cassette. An expression cassette can be introduced into prokaryotic and/or eukaryotic cells and can provide for a high level of expression of the gene encoded by the first and/or Second DNA sequence. The invention also provides a method for Screening other Chlorella virus genes for promoters that can function to express a heterologous gene in prokaryotic and/or eukaryotic hosts

Biochemical Changes During the Growth of Fungi: I. Nitrogen Compounds and Carbohydrate Changes in \u3ci\u3ePenicillium atrovenetum\u3c/i\u3e

Changes in the biochemical constituents of cells were studied during the growth and development of Penicillium atrovenetum. Growth of the fungus, as measured by the dry weight, could be divided into four phases: lag, log, stationary, and death. The percentages of total nitrogen, cold trichloroacetic acid-soluble nitrogen, ribonucleic acid (RNA), and protein increased to a maximum during the lag phase, and subsequently decreased as the fungus aged. The percentage of deoxyribonucleic acid (DNA) was always slightly higher in the spores than in the mycelium. The DNA in the mycelium decreased in the lag phase, and then increased slightly to a plateau for the duration of the log phase, followed by a decrease to a constant percentage during the stationary and death phases. Carbohydrates were present in higher concentration in the mycelium than in the spores. The percentage of carbohydrates in the mycelium increased continually until it reached a maximum late in the log phase, and then decreased as the fungus entered the death phase. The results reported for this fungus are, in general, in agreement with those reported for other microorganisms. Namely, the percentages of enzyme-forming compounds, such as amino acids, nucleotides, RNA, and protein, were highest in the lag phase, whereas storage compounds such as carbohydrates increased to a maximum near the end of the log phase. The definition of log phase in fungi depends on the criteria that are used. If, instead of using the linear increase in dry weight to delimit this growth period, one uses the end of net protein, RNA, and DNA synthesis, a more realistic concept of growth emerges

Biography of James L. Van Etten

Green algae, in surface layers of almost every lake or stream, are some of the most common aquatic creatures. However, unbeknownst to researchers until recently, viruses that infect algae are almost as widespread. Entire ecosystems of algal hosts and their corresponding viruses lay hidden until the 1980s, when James L. Van Etten, a professor of plant pathology at the University of Nebraska (Lincoln), and his colleague Russ Meints discovered and began to characterize the first member of what is now a rapidly expanding family of algal viruses. Van Etten and his colleagues have continued to study these intriguing viruses, focusing on those that infect Chlorella and other similar green algae. The chlorella viruses have many unusual properties, ranging from their large genome sizes to unique modifications in their DNA

Biography of James L. Van Etten

Green algae, in surface layers of almost every lake or stream, are some of the most common aquatic creatures. However, unbeknownst to researchers until recently, viruses that infect algae are almost as widespread. Entire ecosystems of algal hosts and their corresponding viruses lay hidden until the 1980s, when James L. Van Etten, a professor of plant pathology at the University of Nebraska (Lincoln), and his colleague Russ Meints discovered and began to characterize the first member of what is now a rapidly expanding family of algal viruses. Van Etten and his colleagues have continued to study these intriguing viruses, focusing on those that infect Chlorella and other similar green algae. The chlorella viruses have many unusual properties, ranging from their large genome sizes to unique modifications in their DNA

Synthesis and Localization of a Development-Specific Protein in Sclerotia of \u3ci\u3eSclerotinia sclerotiorum\u3c/i\u3e

A development-specific protein (SSP) makes up about 35 to 40% of the total protein in sclerotia of the fungus Sclerotinia sclerotiorum. The protein consists of three charge isomers, with one isomer making up 80 to 90% of the total. In vitro translation of poly(A)+ RNA isolated from cells in early stages of sclerotia formation revealed that 44% of the amino acids incorporated was into SSP. In vivo- and in vitro-synthesized forms of SSP migrated at identical rates on both isoelectric focusing and denaturing polyacrylamide gels, indicating that SSP was not synthesized as a larger precursor. This was significant because SSP accumulated in membrane-bound, organellelike structures which resemble protein bodies found in seeds of many higher plants