A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses

Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A 'taxon duplication' approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily.     

Brazilian isolates of Clonostachys rosea: colonization under different temperature and moisture conditions and temporal dynamics on strawberry leaves

Aims: In a research programme for managing diseases caused by Botryis cinerea, four isolates of the antagonistic fungus Clonostachys rosea (Cr) were obtained from different ecosystems in Brazil. We studied ecological requirements for the colonization of strawberry leaves by these isolates. Methods and Results: Temperature effects on both mycelial growth in vitro and leaf colonization by Cr were studied. At 10°C, growth on potato dextrose agar and colonization of leaf discs were poor. Optimum temperature for mycelial growth and leaf colonization was around 25°C. The isolates were applied to leaves which were exposed to 0–48 h intervals of moisture. They were also applied to leaves which remained from 0 to 36 h without wetness. All isolates efficiently colonized leaves, regardless of moisture interval or the delay to begin wetness. Although all isolates survived in green leaves of whole plants, colonization decreased throughout a 49‐day period. Conclusions: Brazilian isolates of Cr can establish and colonize strawberry leaves under a wide range of temperature and moisture conditions. Significance and Impact of the Study: It is expected that the Brazilian isolates of Cr will establish efficiently in strawberry leaves where they can compete with B. cinerea.     

Altenusin, a biphenyl isolated from the endophytic fungus Alternaria sp., inhibits trypanothione reductase from Trypanosoma cruzi

Parasitic protozoan species belonging to the genera Trypanosoma and Leishmania are the etiological agents of several diseases in tropical areas of the world, for which there is an urgent need for effective and affordable treatment. In this regard, we are screening the Brazilian biodiversity, especially its flora and mycota, for natural products that could serve as leads for drug development against these diseases. Trypanothione reductase (TR) is an enzyme involved in the protection of Trypanosoma and Leishmania species against oxidative stress, and is considered to be a validated drug target. The endophytic fungus Alternaria sp. (UFMGCB55) was isolated from the plant Trixis vauthieri DC (Asteraceae), known to contain trypanocidal compounds. The organic extract of the culture of Alternaria sp. was able to inhibit TR by 99%, when tested at 20 microg mL(-1). Fractionation of the extract identified altenusin, a biphenyl derivative with an IC50 value of 4.3+/-0.3 microM in the TR assay. This compound is the first in its class to have shown TR inhibitory activity, opening new perspectives for the design of more effective derivatives that could serve as drug leads for new chemotherapeutic agents to treat trypanosomiasis and leishmaniasis.     

High resolution studies of the Afa/Dr adhesin DraE and its interaction with chloramphenicol

Pathogenic Escherichia coli expressing Afa/Dr adhesins are able to cause both urinary tract and diarrheal infections. The Afa/Dr adhesins confer adherence to epithelial cells via interactions with the human complement regulating protein, decay accelerating factor (DAF or CD55). Two of the Afa/Dr adhesions, AfaE-III and DraE, differ from each other by only three residues but are reported to have several different properties. One such difference is disruption of the interaction between DraE and CD55 by chloramphenicol, whereas binding of AfaE-III to CD55 is unaffected. Here we present a crystal structure of a strand-swapped trimer of wild type DraE. We also present a crystal structure of this trimer in complex with chloramphenicol, as well as NMR data supporting the binding position of chloramphenicol within the crystal. The crystal structure reveals the precise atomic basis for the sensitivity of DraE-CD55 binding to chloramphenicol and demonstrates that in contrast to other chloramphenicol-protein complexes, drug binding is mediated via recognition of the chlorine "tail" rather than via intercalation of the benzene rings into a hydrophobic pocket.     

An atomic resolution model for assembly, architecture, and function of the Dr adhesins

Pathogenic bacteria possess adhesion protein complexes that play essential roles in targeting host cells and in propagating infection. Although each family of adhesion proteins is generally associated with a specific human disease, the Dr family from Escherichia coli is a notable exception, as its members are associated with both diarrheal and urinary tract infections. These proteins are reported to form both fimbrial and afimbrial structures at the bacterial cell surface and target a common host cell receptor, the decay-accelerating factor (DAF or CD55). Using the newly solved three-dimensional structure of AfaE, we have constructed a robust atomic resolution model that reveals the structural basis for assembly by donor strand complementation and for the architecture of capped surface fibers.     

Voltage-dependent inactivation of slow calcium channels in intact twitch muscle fibers of the frog

Inactivation of slow Ca2+ channels was studied in intact twitch skeletal muscle fibers of the frog by using the three-microelectrode voltage-clamp technique. Hypertonic sucrose solutions were used to abolish contraction. The rate constant of decay of the slow Ca2+ current (ICa) remained practically unchanged when the recording solution containing 10 mM Ca2+ was replaced by a Ca2+-buffered solution (126 mM Ca-maleate). The rate constant of decay of ICa monotonically increased with depolarization although the corresponding time integral of ICa followed a bell-shaped function. The replacement of Ca2+ by Ba2+ did not result in a slowing of the rate of decay of the inward current nor did it reduce the degree of steady-state inactivation. The voltage dependence of the steady-state inactivation curve was steeper in the presence of Ba2+. In two-pulse experiments with large conditioning depolarizations ICa inactivation remained unchanged although Ca2+ influx during the prepulse greatly decreased. Dantrolene (12 microM) increased mechanical threshold at all pulse durations tested, the effect being more prominent for short pulses. Dantrolene did not significantly modify ICa decay and the voltage dependence of inactivation. These results indicate that in intact muscle fibers Ca2+ channels inactivate in a voltage-dependent manner through a mechanism that does not require Ca2+ entry into the cell.     

The Cure Rate after Placebo or No Therapy in American Cutaneous Leishmaniasis: A Systematic Review and Meta-Analysis

Introduction

There are few drugs with proven efficacy in cutaneous leishmaniasis (CL), and pentavalent antimonial derivatives are still the main first-line therapeutic agents worldwide, despite their recognized high toxicities. Randomized controlled clinical trials assessing the efficacy and safety of new therapeutic modalities are of high priority, and the definition of the design of such trials raises debate about the use of placebo as a comparator. To support the use of placebo as a comparator, two main points need to be addressed: 1- the cure rate without any therapeutic intervention and 2- the damage caused by CL and its impact on patients.

Objective

The aim of this study was to systematically assess the spontaneous cure rate for American CL and to broaden the discussion about placebo use in CL trials.

Methods

The PRISMA guidelines for systematic reviews and the Cochrane manual were followed. The sources used were the PubMed and LILACS databases. Studies were included if they reported cure rates using placebo or no treatment in American CL.

Results

Thirteen studies of a total of 352 patients were ultimately included in this review. The summarized global cure rates for all Leishmania species according to the intention-to-treat analyses performed at approximately three (“initial cure”) and nine (“definitive cure”) months after “no treatment” or placebo use were 26% (CI95%: 16 to 40%) and 26% (CI95%:16 to 38%), respectively. Notably, a significantly lower cure rate was observed for L. braziliensis infection (6.4%, CI95%:0.2 to 20%) than for L. mexicana infection (44%, CI95%:19 to 72%), p = 0.002. Of note, relapse occurred in 20% of patients with initial healing (CI95%:9.2 to 38.9%).

Conclusion

These results clearly demonstrate a low spontaneous cure rate following no-treatment or placebo use, confirming that this strategy for the control group in CL studies expose patients to greater morbidity, especially for CL caused by L. braziliensis. Therefore, from this point, the crucial questionto consider regarding placebo use isthe seriousness of the suffering caused by this disease.     

A FURTHER CONTRIBUTION TO CLOSED-CONE PINE (OOCARPAE) HISTORY

A new record of a fossil Monterey pine (Pinus radiata D. Don) is recorded from rocks of the Plio-Pleistocene age, southern California, and the affinities of other presumed fossil closed-cone pines are revised. This has led to the recognition of two new pine species, Pinus storeyana Axelrod of subsect. Oocarpae and Pinus verdiana Axelrod of subsect. Ponderosae. Geologic evidence indicates that forerunners of the present California and Mexican species of Oocarpae were in proximity in Mexico during the Miocene. They were isolated following opening of the Gulf of California, the northward movement of Baja and Alta California on the San Andreas fault system, and the spread of desert climate. New populations of Pinus radiata developed during the Pliocene (5–2 million years) and later as environmental diversity increased. This also enabled Pinus remorala Mason and P. muricata D. Don, which the fossil record suggests were distinct into the Late Pleistocene, to hybridize in the new topographic-climatic Holocene environments.     

Temperature effects on sex differentiation of two South American atherinids, Odontesthes argentinensis and Patagonina hatcheri

Synopsis The present study investigated the effects of water temperature (18, 21, and 25 °C) on the histological process of gonadal sex differentiation of two commercially important atherinid fishes from South America, Odontesthes argentinensis (sea pejerrey) and Patagonina hatcheri (Patagonian freshwater pejerrey). In both species, female gonadal sex differentiation began with the formation of lateral stromal cell outgrowths and the appearance of meiotic oocytes. The male gonads remained quiescent for about twice as long as the female gonads, with differentiation becoming evident by the formation of the main sperm duct and of cysts of germ cells at the periphery of the gonads. Meiosis in males occurred relatively long after somatic differentiation of the testis. The ovaries of O. argentinensis differentiated at 28 days (20.3 mm) at 25 °C, 42 days (24.0 mm) at 21 °C, and 56 days (23.8 mm) at 18 °C. In the males, differentiation was observed at 98 days at 25 and 21 °C (39.4 mm and 40.4 mm, respectively), but at 112 days under 18 °C (40.7 mm). In P. hatcheri, differentiation of females occurred at 21 days (17.8 mm) at 25 °C, 28 days (20.8 mm) at 21 °C, and 35 days (23.2 mm) at 18 °C. Male differentiation became evident at 56 days under 25 and 21 °C (30.8 and 32.7 mm, respectively), and at 70 days (37.7 mm) at 18 °C. The sex-ratios of O. argentinensis reared at 18 or 21 °C were female-biased whereas those at 25 °C were not; groups reared at 18 °C had significantly more females than groups from the same progeny reared at 25 °C. In contrast, the sex-ratios in all groups of P. hatcheri did not differ significantly from 1:1 and no significant differences were found between groups of the same progeny reared at different temperatures. These results suggest the occurrence of thermolabile sex determination (TSD) in O. argentinensis whereas in P. hatcheri gonadal sex appears to be strongly genetically determined.     

Quantification of yield losses caused by leaf anthracnose on sorghum in Brazil

The leaf anthracnose disease in sorghum, caused by Colletotrichum sublineolum (Henn. ex Sacc. & Trotter), is widely distributed throughout its Brazilian cultivation areas. The disease can cause significant losses in grain yield and quality. This study aimed to quantify the effects of leaf anthracnose on grain yield of different sorghum genotypes. Two elite inbred lines of sorghum, BR009 (susceptible) and BR008 (moderately resistant), and the hybrids, BR304 and MR43 (susceptible), BRS310 and DKB599 (moderately resistant) and BRS308 and AG1060 (resistant), were planted in a complete randomized block design with three replicates. The disease severity (DS) was evaluated weekly, starting from the onset of the first foliar symptoms, and yield losses were estimated using linear regression analysis. Leaf anthracnose significantly reduced sorghum yields in the susceptible genotypes. The highest yield loss of 86% was observed in the inbred line BR009, when the disease severity reached 100%. For the hybrids, the grain yield loss varied from 35% (BRS310) to 72% (BRS308). According to the adjusted model, a grain yield reduction of 23.48 kg/ha for BR304, 14.57 kg/ha for BRS310 and 15.91 kg/ha for DKB599 was observed for every 1% increase in disease severity. We demonstrate for the first time the effect of leaf anthracnose disease on grain sorghum yields under Brazilian conditions. The results from this study provide a starting point for developing new strategies for the integrated disease management of sorghum anthracnose.