The Type Ia supernova 2004s, a clone of SN 2001el, and the optimal photometric bands for extinction estimation

We present optical (UBVRI) and near-IR (YJHK) photometry of the normal Type Ia supernova (SN) 2004S. We also present eight optical spectra and one near-IR spectrum of SN 2004S. The light curves and spectra are nearly identical to those of SN 2001el. This is the first time we have seen optical and IR light curves of two Type Ia SNe match so closely. Within the one parameter family of light curves for normal Type Ia SNe, that two objects should have such similar light curves implies that they had identical intrinsic colors and produced similar amounts of Ni-56. From the similarities of the light-curve shapes we obtain a set of extinctions as a function of wavelength that allows a simultaneous solution for the distance modulus difference of the two objects, the difference of the host galaxy extinctions, and RV. Since SN 2001el had roughly an order of magnitude more host galaxy extinction than SN 2004S, the value of R-V = 2.15(-0.22)(+0.24) pertains primarily to dust in the host galaxy of SN 2001el. We have also shown via Monte Carlo simulations that adding rest-frame J-band photometry to the complement of BVRI photometry of Type Ia SNe decreases the uncertainty in the distance modulus by a factor of 2.7. A combination of rest-frame optical and near-IR photometry clearly gives more accurate distances than using rest-frame optical photometry alone.

Porcine Circovirus Type 2 Morphogenesis in a Clone Derived from the L35 Lymphoblastoid Cell Line

Porcine circovirus type 2 (PCV2) is the essential infectious agent of post-weaning multisystemic wasting syndrome (PMWS), one of the most important diseases of swine. Although several studies have described different biological properties of the virus, some aspects of its replication cycle, including ultrastructural alterations, remain unknown. The aim of the present study was to describe for the first time a complete morphogenesis study of PCV2 in a clone of the lymphoblastoid L35 cell line at the ultrastructural level using electron microscopy techniques. Cells were infected with PCV2 at a multiplicity of infection of 10 and examined at 0, 6, 12, 24, 48, 60 and 72 h post-infection. PCV2 was internalized by endocytosis, after which the virus aggregated in intracytoplasmic inclusion bodies (ICIs). Subsequently, PCV2 was closely associated with mitochondria, completing a first cytoplasmic phase. The virus entered the nucleus for replication and virus assembly and encapsidation occurred with the participation of the nuclear membrane. Immature virions left the nucleus and formed ICIs in a second cytoplasmic phase. The results suggest that at the end of the replication cycle (between 24 and 48 h), PCV2 was released either by budding of mature virion clusters or by lysis of apoptotic or dead cells. In conclusion, the L35-derived clone represents a suitable in-vitro model for PCV2 morphogenesis studies and characterization of the PCV2 replication cycle. (C) 2010 Elsevier Ltd. All rights reserved.

Le testateur et son clone inavoué, le juge : clone difforme ou conforme dans la recherche des intentions du testateur : le juge et l’interprétation des volontés du testateur

Un résumé est également disponible en anglais.

Le testateur et son clone inavoué, le juge ou l'art de concilier formalisme et volontarisme dans l'interprétation testamentaire: à la recherche du sens des expressions ou des institutions juridiques auxquelles fait référence le testateur

Article publié avec l'autorisation de la Chambre des notaires du Québec.

Evidence of evolving extraintestinal enteroaggregative Escherichia coli ST38 clone

BACKGROUND: Several clones of extended-spectrum β-lactamase (ESBL)–producing extraintestinal pathogenic Escherichia coli (ExPEC) have globally expanded their distribution. ExPEC infections often originate from the patient’s own intestinal flora, although the degree of overlap between diarrheagenic E. coli and ExPEC pathotypes is unclear. Relatively little is known about antimicrobial drug resistance in the most common diarrheagenic E. coli groups, including enteroaggregative E. coli (EAEC), and bacterial gastroenteritis is generally managed without use of antimicrobial drugs. APPROACHES: We conducted this study to establish the presence and characteristics of ESBL-producing EAEC in a well-defined collection of ESBL-producing isolates. The isolates were from human and animal sources in Germany, the Netherlands, and the United Kingdom. DNA from 359 ESBL isolates was screened for the presence of the EAEC transport regulator gene (aggR), located on the EAEC plasmid, using a real-time PCR assay and the phylogroup was determined for each positive isolate. A microarray was used to detect ESBL genes, such as blaCTX-M, at the group level, as previously described. The antimicrobial drug susceptibilities of EAEC isolates were determined and virulence factors associated with intestinal and extraintestinal infection and with EAEC were investigated . RESULTS AND CONCLUSIONS: We assigned a virulence score (total number of virulence factor genes detected; maximum possible score 22) and a resistance score (total number of drug classes; maximum score 11) to each isolate. We isolated 11 EAEC from humans. Eight of the EAEC were isolated from urine specimens, and 1 was isolated from a blood culture; 63% belonged to phylogroup D (Table). EAEC ST38, the most common (55%) ST, was significantly associated with extraintestinal sites in the subset of 140 human isolates (Fisher exact test, p<0.0001)

Plasmodium vivax: Microsatellite analysis of multiple-clone infections

We used mixtures of genomic DNA from two genetically distinct isolates from Brazil, 42M and 312M, to investigate how accurately 12-locus microsatellite typing describes the overall genetic diversity and characterizes multilocus haplotypes in multiple-clone Plasmodium vivax infections. We found varying PCR amplification efficiencies of microsatellite alleles; for example, from the same 1:1 mixture of 42M and 312M DNA we amplified predominantly 312M-type alleles at 10 loci and 42M-type alleles at 2 loci. All microsatellite alleles were accurately scored in 1:0.5 and 1:0.25 312M:42M DNA mixtures, even when minor peak heights did not meet previously suggested criteria for minor allele detection in multiple-clone infections. Relative proportions of major and minor alleles were unaffected by multiple displacement amplification of template DNA prior to PCR-based microsatellite typing. Although microsatellite typing may detect minor alleles in clone mixtures, amplification biases may lead to inaccurate assignment of predominant haplotypes in multiple-clone P. vivax infections. (C) 2008 Elsevier Inc. All rights reserved.

KClone: A Proposed Approach to Fast Precise Code Clone Detection

In all applications of clone detection it is important to have precise and efficient clone identification algorithms. This paper proposes and outlines a new algorithm, KClone for clone detection that incorporates a novel combination of lexical and local dependence analysis to achieve precision, while retaining speed. The paper also reports on the initial results of a case study using an implementation of KClone with which we have been experimenting. The results indi- cate the ability of KClone to find types-1,2, and 3 clones compared to token-based and PDG-based techniques. The paper also reports results of an initial empirical study of the performance of KClone compared to CCFinderX.

Produtividade e qualidade dos frutos da laranjeira 'Pêra' clone IAC em 16 porta-enxertos na região de Bebedouro-SP

Avaliou-se a influência de 16 porta-enxertos na produtividade, nas características físicas e químicas (sólidos solúveis totais-°Brix; acidez; ratio; porcentagem de suco; índice tecnológico e tamanho dos frutos) dos frutos da laranjeira 'Pêra' [Citrus sinensis (L.) Osbeck] e na incidência e severidade da clorose variegada dos citros (CVC). O plantio do experimento foi realizado em julho de 1993, com espaçamento de 6,0 m entre linhas e 3,5 m entre plantas (476 plantas/ha). O experimento foi conduzido sem irrigação. O delineamento experimental foi em blocos ao acaso, duas plantas por parcela, três repetições e 16 tratamentos, constituídos pelas seguintes cultivares porta-enxertos: tangerineira 'Sun Chu Sha Kat' (Citrus reticulata Blanco), tangerineira 'Pectinífera' (C. reticulata), 'Shekwasha' (C. depressa Hayata), tangerineira 'Pectinífera/Shekwasha' (C. depressa Hayata), tangerineira 'Batangas' (C. reticulata), tangerineira 'Oneco' (C. reticulata), citrangor [citrange (Poncirus trifoliata Raf. x C. sinensis) x C. sinensis], citrandarin [C.sunki hort. Ex Tanaka) x Poncirus trifoliata (L.) Raf. cv. English, tangerineira 'Sunki' (C. sunki), tangerineira 'Suen-Kat' (C. sunki), tangerineira 'Nasnaran' (C. amblycarpa Ochse), tangerineira 'Venezuela' (C. reticulata), tangerineira Heen Naran (C. lycopersicaeformis hort. ex Tan. ), limoeiro 'Cravo' (C. limonia Osbeck) x tangerineira 'Cleópatra' (C. reshni hort ex Tanaka), limoeiro 'Cravo' (C. limonia), tangerineira 'Cleópatra' (C. reshni). A intensidade da clorose variegada dos citros variou em função dos porta-enxertos e não se relacionou com a produção de frutos até a quarta safra. Os porta-enxertos estudados, com exceção da tangerineira Nasnaran, proporcionaram qualidade e produções iniciais de frutos similares aos do limoeiro 'Cravo'.

Plants of an Eucalyptus clone damaged by Scolytidae and Platypodidae (Coleoptera)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Nutrient cycling in a RRIM 600 clone rubber plantation

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Identification of bacteria in endodontic infections by sequence analysis of 16S rDNA clone libraries

A significant proportion of oral bacteria are unable to undergo cultivation by existing techniques. In this regard, the microbiota from root canals still requires complementary characterization. The present study aimed at the identification of bacteria by sequence analysis of 16S rDNA clone libraries from seven endodontically infected teeth. Samples were collected from the root canals, subjected to the PCR with universal 16S rDNA primers, cloned and partially sequenced. Clones were clustered into groups of closely related sequences (phylotypes) and identification to the species level was performed by comparative analysis with the GenBank, EMBL and DDBJ databases, according to a 98 % minimum identity. All samples were positive for bacteria and the number of phylotypes detected per subject varied from two to 14. The majority of taxa (65(.)2 %) belonged to the phylum Firmicutes of the Gram-positive bacteria, followed by Proteobacteria (10(.)9 %), Spirochaetes (4(.)3 %), Bacteroidetes (6(.)5 %), Actinobacteria (2(.)2 %) and Deferribacteres (2(.)2 %). A total of 46 distinct taxonomic units was identified. Four clones with low similarity to sequences previously deposited in the databases were sequenced to nearly full extent and were classified taxonomically as novel representatives of the order Clostridiales, including a putative novel species of Mogibacterium. The identification of novel phylotypes associated with endodontic infections suggests that the endodontium may still harbour a relevant proportion of uncharacterized taxa.

Somatic meiosis and development of the juvenile gametophyte in members of the Batrachospermales sensu lato (Rhodophyta)

Seven populations (six in culture and one sampled directly from nature) of the freshwater red algal families Batrachospermaceae, Lemaneaceae and Thoreaceae were examined, involving three species of Batrachospermum, two of Paralemanea and one of Thorea. All 'Chantransia' stages ultimately produced juvenile gametophytes. The production of juvenile gametophytes in the three populations of Batrachospermum was generally most abundant at 15°C and low irradiances (47-68 μmol photons m-2 s-1). The most abundant gametophyte development in the Paralemanea species was observed at 10°C and low or high irradiances (47-142 μmol photons m-2 s-1). Gametophyte production in Thoreaceae occurred at higher temperatures (20°C) and also at low irradiances. In species of the Batrachospermaceae and Lemaneaceae, the 'elimination cells' can be situated on the basal or suprabasal cell of the juvenile gametophyte, but the position is usually fixed in individual species. The presence and position of the elimination cells remain to be established in Thoreaceae. Our results corroborate a previous study suggesting that the position of elimination cells is such a constant feature that it is of potential diagnostic value at the generic or infrageneric (sectional or specific) level. The characteristics observed in the development of the juvenile gametophytes in species of Batrachospermaceae and Lemaneaceae essentially agreed with general descriptions in the previous studies. The characteristics of the Thoreaceae, with a distinctive developmental pattern of the juvenile gametophyte and the occurrence of two morphological types in the 'Chantransia' stage, support the proposal to elevate it to the ordinal level. Two remarkable observations in Batrachospermum species were the production of numerous juvenile gametophytes from filaments of the same plant of the 'Chantransia' stage and the formation of a system of rhizoidal filaments or cell agglomeration of the juvenile gametophytes, which produced new gametophytes. These two characteristics potentially increase the formation of additional gametophytes under favourable conditions.

Ecology and morphological characterization of gametophyte and 'Chantransia' stages of Sirodotia huillensis (Batrachospermales, Rhodophyta) from a stream in central Mexico

The morphology and phenology of Sirodotia huillensis was evaluated seasonally in a central Mexican first-order calcareous stream. Water temperature was constant (24-25°C) and pH circumneutral to alkaline (6.7-7.9), and calcium and sulfates were the dominant ions. The gametophyte stages were characterized by the presence of a distinctive mucilaginous layer, a marked difference in phycocyanin to phycoerythrin ratio between female and male plants, and the presence of a carpogonia with a large trichogyne (>60 μm). Occasionally three capogonia were observed on a single basal cell. The 'Chantransia' stages were morphologically similar to those described for the other members of Batrachospermales. A remarkable observation was the formation of dome-shaped structures, consisting of prostrate filaments that are related with the development of new gametophytes. Chromosome numbers were n = 4 for fascicle cells, cortical filament cells and dome-shaped cells, and 2n = 8 for gonimoblast filament cells and 'Chantransia' stage filaments. Gametophytes and 'Chantransia' stages occurred in fast current velocities (60-170 cm/s) and shaded (33.1-121 μmol photons/m2/s) stream segments. The population fluctuated throughout the study period in terms of percentage cover and frequency: the 'Chantransia' stages were most abundant in the rainy season, whereas gametophytic plants had the highest frequency values during the dry season. These results were most likely a result of fluctuations in rainfall and related changes in current velocity. Some characteristics of this population can be viewed as probable adaptations to high current velocities: the mucilaginous layer around plants that reduces drag; potential increase in fertilization by the elongate and plentiful trichogynes and abundant dome-shaped structures producing several gametophytes.