Phylogenetic Relationships Within the Centothecoideae + Panicoideae Clade (Poaceae) Based on ndhF and rpl16 Intron Sequences and Structural Data

The PACCAD clade (Panicoideae, Arundinoideae, Chloridoideae, Centothecoideae, Aristidoideae, Danthonioideae) is well supported in all recent studies of Poaceae. However, phylogenetic relationships within the clade are still unresolved, although several branches are strongly supported. In this study, we focus on the phylogeny of the Centothecoideae + Panicoideae clade, one of the major lineages within the PACCAD clade, and one of the most diverse in the family. Two previously unsampled tribes, Isachneae and Steyermarkochloeae, are included, as are additional taxa of Centothecoideae. Phylogenetic analyses of plastid genome sequences (ndhF gene and rpl16 intron) and structural data show increased support of the centothecoid–panicoid clade, but phylogenetic relationships between the two putative subfamilies remain unresolved. Centothecoideae may be sister to Panicoideae or they may be paraphyletic with respect to Panicoideae, as monophyly of Centothecoideae is weakly supported at best. Polyphyly of Panicoideae is demonstrated as Isachneae and Steyermarkochloeae (only with ndhF) form well-supported clades with Micraira–Eriachne and Chasmanthium, respectively. Polyphyly of Arundinelleae is also confirmed as Danthoniopsis and related genera resolve elsewhere. Centothecoideae, as recently circumscribed, resolve as three strongly supported clades including Danthoniopsis and related genera. Cyperochloa (previously incertae sedis) and arundinoid Spartochloa are sister and fall within the centothecoids with strong support. Centotheceae are polyphyletic and segregate into three major groups. One centothecoid genus, Zeugites, is demonstrably paraphyletic

Phylogenetic Relationships Among the One-Flowered, Determinate Genera of Bambuseae (Poaceae: Bambusoideae)

Bambuseae (woody bamboos), one of two tribes recognized within Bambusoideae (true bamboos), comprise over 90% of the diversity of the subfamily, yet monophyly of the tribe is generally only moderately supported, and phylogenetic relationships within the tribe are poorly understood. In addition, there appears to be some level of conflict between morphological and molecular data within the tribe. We conducted a parsimony analysis of 43 species of Bambuseae, three of Olyreae (herbaceous bamboos), and two outgroup taxa using morphological and plastid rpl16 intron sequence data to (1) further test the monophyly of Bambuseae, (2) test the monophyly of Chusqueinae and Hickelinae (the two one-flowered, determinate subtribes), and (3) examine the apparent conflict between molecular and morphological data sets in the determinate, one-flowered genera of Bambuseae. We recovered a monophyletic Bambusoideae, Bambuseae, Olyreae, and Chusqueinae, although support for Bambuseae remained moderate. Our results suggest that the morphological similarities between Chusqueinae and Hickelinae are homoplasious, but robust resolution of relationships among the major lineages of woody bamboos is still wanting

Phylogeny of the Grasses (Poaceae) Revisited

The most robust previously published phylogeny for the overall structure of the grass family (Poaceae) shows three early diverging lineages and two major derived clades, the BEP clade and the PACCAD clade (Grass Phylogeny Working Group 2001). A few key taxa were incompletely sampled, however, and support for the BEP clade was moderate at best and relationships among the major lineages within the PACCAD clade remained unresolved. In addition, recent studies indicated that the sister group to Poaceae may be Joinvilleaceae and/or Ecdeiocoleaceae, the latter of which were not previously sampled. In this study, missing structural data were determined and analyzed as well as sequence data for ndhF and rbcL, the two most complete plastid sequence data sets. Sampling was increased with a particular focus on key taxa such as Danthoniopsis, Eriachne, Micraira, and Streptogyna and a representative of the outgroup, Ecdeiocoleaceae. A total of 61 ingroup and two outgroup taxa were analyzed using maximum parsimony for total data, and maximum parsimony, Bayesian inference, and neighbor joining for the molecular data. A strongly supported clade of ((Eriachneae, Isachne) Micraira) was recovered as a sister subfamily to Arundinoideae and excluded from Panicoideae. Arundinaria was strongly united with Bambusoideae. The position of Streptogyna was weakly supported among Ehrhartoideae, and is still unresolved. An outgroup effect on ingroup topology was observed, demonstrating that highly divergent outgroups may unpredictably alter ingroup relationships

Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005

BACKGROUND The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.This work was partially supported by salaries from the NOAA Coral Reef Conservation Program to the NOAA Coral Reef Conservation Program authors. NOAA provided funding to Caribbean ReefCheck investigators to undertake surveys of bleaching and mortality. Otherwise, no funding from outside authors' institutions was necessary for the undertaking of this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

An A91V SNP in the perforin gene is frequently found in NK/T-cell lymphomas

NK/T-cell lymphoma (NKTCL) is the most frequent EBV-related NK/T-cell disease. Its clinical manifestations overlap with those of familial haemophagocytic lymphohistiocytosis (FHLH). Since PERFORIN (PRF1) mutations are present in FHLH, we analysed its role in a series of 12 nasal and 12 extranasal-NKTCLs. 12.5% of the tumours and 25% of the nasal-origin cases had the well-known g.272C>T(p.Ala91Val) pathogenic SNP, which confers a poor prognosis. Two of these cases had a double-CD4/CD8-positive immunophenotype, although no correlation was found with perforin protein expression. p53 was overexpressed in 20% of the tumoral samples, 80% of which were of extranasal origin, while none showed PRF1 SNVs. These results suggest that nasal and extranasal NKTCLs have different biological backgrounds, although this requires validation

Biology of moderately halophilic aerobic bacteria

The moderately halophilic heterotrophic aerobic bacteria form a diverse group of microorganisms. The property of halophilism is widespread within the bacterial domain. Bacterial halophiles are abundant in environments such as salt lakes, saline soils, and salted food products. Most species keep their intracellular ionic concentrations at low levels while synthesizing or accumulating organic solutes to provide osmotic equilibrium of the cytoplasm with the surrounding medium. Complex mechanisms of adjustment of the intracellular environments and the properties of the cytoplasmic membrane enable rapid adaptation to changes in the salt concentration of the environment. Approaches to the study of genetic processes have recently been developed for several moderate halophiles, opening the way toward an understanding of haloadaptation at the molecular level. The new information obtained is also expected to contribute to the development of novel biotechnological uses for these organisms

Dengue Virus Type 2 Infections of Aedes aegypti Are Modulated by the Mosquito's RNA Interference Pathway

A number of studies have shown that both innate and adaptive immune defense mechanisms greatly influence the course of human dengue virus (DENV) infections, but little is known about the innate immune response of the mosquito vector Aedes aegypti to arbovirus infection. We present evidence here that a major component of the mosquito innate immune response, RNA interference (RNAi), is an important modulator of mosquito infections. The RNAi response is triggered by double-stranded RNA (dsRNA), which occurs in the cytoplasm as a result of positive-sense RNA virus infection, leading to production of small interfering RNAs (siRNAs). These siRNAs are instrumental in degradation of viral mRNA with sequence homology to the dsRNA trigger and thereby inhibition of virus replication. We show that although dengue virus type 2 (DENV2) infection of Ae. aegypti cultured cells and oral infection of adult mosquitoes generated dsRNA and production of DENV2-specific siRNAs, virus replication and release of infectious virus persisted, suggesting viral circumvention of RNAi. We also show that DENV2 does not completely evade RNAi, since impairing the pathway by silencing expression of dcr2, r2d2, or ago2, genes encoding important sensor and effector proteins in the RNAi pathway, increased virus replication in the vector and decreased the extrinsic incubation period required for virus transmission. Our findings indicate a major role for RNAi as a determinant of DENV transmission by Ae. aegypti