Genomic Patterns of Positive Selection at the Origin of Rust Fungi

Understanding the origin and evolution of pathogenicity and biotrophic life-style of rust fungi has remained a conundrum for decades. Research on the molecular mechanisms responsible for rust fungi evolution has been hampered by their biotrophic life-style until the sequencing of some rust fungi genomes. With the availability of multiple whole genomes and EST data for this group, it is now possible to employ genome-wide surveys and investigate how natural selection shaped their evolution. In this work, we employed a phylogenomics approach to search for positive selection and genes undergoing accelerated evolution at the origin of rust fungi on an assembly of single copy genes conserved across a broad range of basidiomycetes. Up to 985 genes were screened for positive selection on the phylogenetic branch leading to rusts, revealing a pervasive signal of positive selection throughout the data set with the proportion of positively selected genes ranging between 19.6–33.3%. Additionally, 30 genes were found to be under accelerated evolution at the origin of rust fungi, probably due to a mixture of positive selection and relaxation of purifying selection. Functional annotation of the positively selected genes revealed an enrichment in genes involved in the biosynthesis of secondary metabolites and several metabolism and transporter classes.     

Identification of Chromobacterium violaceum genes with potential biotechnological application in environmental detoxification

Chromobacterium violaceum is a Gram-negative bacterium found in a wide variety of tropical and subtropical ecosystems. The complete genome sequence of C. violaceum ATCC 12472 is now available, and it has considerable biotechnological potential for various applications, such as environmental detoxification, as well as medical and agricultural use. We examined the biotechnological potential of C. violaceum for environmental detoxification. Three operons, comprising the ars operon, involved in arsenic resistance, the cyn operon, involved in cyanate detoxification, and the hcn operon, encoding a cyanase, responsible for biogenic production of cyanide, as well as an open reading frame, encoding an acid dehalogenase, were analyzed in detail. Probable catalytic mechanisms for the enzymes were determined, based on amino acid sequence comparisons and on published structural information for these types of proteins.     

Sperm viability of canine and caprine semen samples preserved in a dry shipper

This study assessed the efficacy of a dry shipper to preserve canine and caprine semen samples. After equilibration, semen straws from six Majorera bucks and five dogs were frozen and stored in liquid nitrogen (LN). Thirty days after freezing, half of the frozen straws were transferred from LN to a dry shipper (DS). Then, thawing was performed at 1, 2, 3, 5 and 7 days and the percentages of motile spermatozoa, acrosome intact spermatozoa and abnormal spermatozoa were determined. The sperm motility (total and progressive) of canine semen samples preserved with DS was quite similar to those preserved in LN, and no significant differences were observed throughout the experimental period. In addition, no differences were observed in the number of abnormal spermatozoa (range: 13.2-19.0%) or intact acrosome (range 91.3-95%) between both storage protocols. Buck semen samples showed equivalent levels of progressive motility (between 50% and 60%) and intact acrosome membrane (around 70%) during the first 3 days of storage in both procedures; however, from the fifth day of storage onwards, a notable decrease in semen quality was observed in the samples preserved in DS, showing a dramatic fall in the semen viability after 7 days of preservation (12.3% and 36.8%, progressive fast spermatozoa and acrosome integrity, respectively). In dog samples, the present study confirmed that seminal quality did not show modifications for the preservation period (7 days), confirming the efficacy of the dry shipper to preserve frozen samples for a short time. However, under the circumstances reported in this study, the sperm quality of buck samples preserved in the dry shipper only held during the first 3 days of storage, and therefore, its practical application could be more limited.     

Fungal Pathogens: The Battle for Plant Infection

The attempted infection of a plant by a pathogen, such as a fungus or an Oomycete, may be regarded as a battle whose major weapons are proteins and smaller chemical compounds produced by both organisms. Indeed, plants produce an astonishing plethora of defense compounds that are still being discovered at a rapid pace. This pattern arose from a multi-million year, ping-pong?type co-evolution, in which plant and pathogen successively added new chemical weapons in this perpetual battle. As each defensive innovation was established in the host, new ways to circumvent it evolved in the pathogen. This complex co-evolution process probably explains not only the exquisite specificity observed between many pathogens and their hosts, but also the ineffectiveness or redundancy of some defensive genes which often encode enzymes with overlapping activities. Plants evolved a complex, multi-level series of structural and chemical barriers that are both constitutive or preformed and inducible. These defenses may involve strengthening of the cell wall, hypersensitive response (HR), oxidative burst, phytoalexins and pathogenesis-related (PR) proteins. The pathogen must successfully overcome these obstacles before it succeeds in causing disease. In some cases, it needs to modulate or modify plant cell metabolism to its own benefit and/or to abolish defense reactions. Central to the activation of plant responses is timely perception of the pathogen by the plant. A crucial role is played by elicitors which, depending on their mode of action, are broadly classified into nonspecific elicitors and highly specific elicitors or virulence effector/avirulence factors. A protein battle for penetration is then initiated, marking the pathogen attempted transition from extracellular to invasive growth before parasitism and disease can be established. Three major types of defense responses may be observed in plants: non-host resistance, host resistance, and host pathogenesis. Plant innate immunity may comprise a continuum from non-host resistance involving the detection of general elicitors to host-specific resistance involving detection of specific elicitors by R proteins. It was generally assumed that non-host resistance was based on passive mechanisms and that nonspecific rejection usually arose as a consequence of the non-host pathogen failure to breach the first lines of plant defense. However, recent evidence has blurred the clear-cut distinction among non-host resistance, host-specific resistance and disease. The same obstacles are also serious challenges for host pathogens, reducing their success rate significantly in causing disease. Indeed, even susceptible plants mount a (insufficient) defense response upon recognition of pathogen elicited molecular signals. Recent evidence suggests the occurrence of significant overlaps between the protein components and signalling pathways of these types of resistance, suggesting the existence of both shared and unique features for the three branches of plant innate immunity.     

Characterisation of polyphenols by HPLC-PAD-ESI/MS and antioxidant activity in Equisetum telmateia

The antioxidant activity of an aqueous extract (infusion) and respective ethyl acetate fraction of Equisetum telmateia Ehrh. (Equisetaceae), a plant used in traditional medicine for its anti-inflammatory and diuretic properties, has been evaluated by DPPH, TEAC and TBARS assays. A high and significant antioxidant activity was detected in the ethyl acetate fraction. Analysis of the aqueous extract and the ethyl acetate fraction by HPLC-PAD-ESI/MS allowed the identification of the major phenolic compounds as flavan-3-ol, kaempferol and phenolic acid derivatives. Among the flavan-3-ols, A-type proanthocyanidins and afzelechin derivatives were detected as well as the more common B-type procyanidins, B2 and C1, whose identification was further confirmed by HPLC using detection involving chemical reaction with p-dimethylamino-cinnamaldehyde. The results suggest that the anti-inflammatory activity of E. telmateia could be due, at least in part, to the presence of compounds with antioxidant activity.     

Winter is coming: Miocene and Quaternary climatic shifts shaped the diversification of Western‐Mediterranean Harpactocrates (Araneae,Dysderidae) spiders

Past climatic shifts have played a major role in generating and shaping biodiversity. Quaternary glacial cycles are the better known examples of dramatic climatic changes endured by ecosystems in temperate regions. Although still a matter of debate, some authors suggest that glaciations promoted speciation. Here we investigate the effect of past climatic changes on the diversification of the ground‐dwelling spider genus Harpactocrates, distributed across the major mountain ranges of the western Mediterranean. Concatenated and species‐tree analyses of multiple mitochondrial and nuclear loci, combined with the use of fossil and biogeographic calibration points, reveal a Miocene origin of most nominal species, but also unravel several cryptic lineages tracing back to the Pleistocene. We hypothesize that the Miocene Climatic Transition triggered major extinction events in the genus but also promoted its subsequent diversification. Under this scenario, the Iberian mountains acted as an island‐like system, providing shelter to Harpactocrates lineages during the climate shifts and favouring isolation between mountain ranges. Quaternary glacial cycles contributed further to the diversification of the group by isolating lineages in peripheral refugia within mountain ranges. In addition, we recovered some unique biogeographic patterns, such as the colonization of the Alps and the Apennines from the Iberian Peninsula.     

Evidence for the co-circulation of dengue virus type 3 genotypes III and V in the Northern region of Brazil during the 2002-2004 epidemics

The reintroduction of dengue virus type 3 (DENV-3) in Brazil in 2000 and its subsequent spread throughout the country was associated with genotype III viruses, the only DENV-3 genotype isolated in Brazil prior to 2002. We report here the co-circulation of two different DENV-3 genotypes in patients living in the Northern region of Brazil during the 2002-2004 epidemics. Complete genomic sequences of viral RNA were determined from these epidemics, and viruses belonging to genotypes V (Southeast Asia/South Pacific) and III were identified. This recent co-circulation of different DENV-3 genotypes in South America may have implications for pathological and epidemiological dynamics.     

Seasonal growth of Mugil liza Valenciennes, 1836 in a tropical estuarine system

Seasonal changes in the abiotic factors and cyclical events – with the reproduction diagnosed by the gonadosomatic index and the energy status diagnosed by the condition index – were estimators of seasonal growth for juvenile and adult lebranche mullets, Mugil liza, during the rainy and dry seasons in a tropical estuarine system of the western south Atlantic. Fish were collected monthly by gillnets of different mesh sizes. Salinity, water temperature (°C) and dissolved oxygen (%) were measured using a multiparameter. Daily rainfall data (mm) were obtained from the National Institute of Meteorology. Seasonal rings were identified and counted in the sagittae otoliths. Relative Marginal Increment (RMI) was calculated to determine the seasonal growth rate. Gonadosomatic Index (GSI) and Condition Index (CI) were assessed separately for juveniles and adults by anova , with time (month) M. liza growth is controlled by annual cycles of biological and abiotic processes. Using general linear models, the seasonal growth rate of M. liza was well predicted by body condition and rainfall for juveniles, and by salinity for adults. Seasonal variation was observed in the Mundaú Lagoon, with rainfall directly or indirectly being the main seasonal factor influencing the cyclical biological fish processes of M. liza.     

Structural-functional role of chloride in photosystem II

Chloride binding in photosystem II (PSII) is essential for photosynthetic water oxidation. However, the functional roles of chloride and possible binding sites, during oxygen evolution, remain controversial. This paper examines the functions of chloride based on its binding site revealed in the X-ray crystal structure of PSII at 1.9 ? resolution. We find that chloride depletion induces formation of a salt bridge between D2-K317 and D1-D61 that could suppress the transfer of protons to the lumen.