Black Yeast Biota in the Mangrove, in Search of the Origin of the Lethargic Crab Disease (LCD)

Knowledge of natural ecology is essential for a better understanding of pathogenicity and opportunism in black yeast-like fungi. Although etiological agents of diseases caused by these fungi are supposed to originate from the environment, their isolation from nature is difficult. This is probably due to their oligotrophic nature, low competitive ability, and, overall, insufficient data on their natural habitat. We obtained environmental samples from mangrove areas where mortalities by lethargic crab disease (LCD) are reported and areas without disease recorded. Isolation of chaetothyrialean black yeasts and relatives was performed using a highly selective protocol. Species-specific primers were used to determine if these isolates represented Exophiala cancerae or Fonsecaea brasiliensis, two proven agents of LCD, in order to test hypotheses about the origin of the disease. Isolates, identified by morphology as Fonsecaea- or Exophiala-like, were tested specific diagnostic markers for the fungi associated with LCD. Although several black fungi were isolated, the main causative agent of the LCD, E. cancerae, was not found. Molecular markers for F. brasiliensis revealed 10 positive bands for isolates from biofilms on mangrove leaves, branches, and aerial roots, of which four were confirmed by ITS sequencing. The absence of E. cancerae in environmental samples suggests that the species is dependent on the crab, as a genuine pathogen, different from F. brasiliensis, which is probably not dependent on the host species, U. cordatus. However, we did not attempt isolation from the marine water, which may represent the pathway of dispersion of the black yeast species between neighbor mangroves.     

Potential geographical distribution of the red palm mite in South America

Among pests that have recently been introduced into the Americas, the red palm mite, Raoiella indica Hirst (Prostigmata: Tenuipalpidae), is the most invasive. This mite has spread rapidly to several Caribbean countries, United States of America, Mexico, Venezuela, Colombia and Brazil. The potential dispersion of R. indica to other regions of South America could seriously impact the cultivation of coconuts, bananas, exotic and native palms and tropical flowers such as the Heliconiaceae. To facilitate the development of efficacious R. indica management techniques such as the adoption of phytosanitary measures to prevent or delay the dispersion of this pest, the objective of this paper was to estimate the potential geographical distribution of R. indica in South America using a maximum entropy model. The R. indica occurrence data used in this model were obtained from extant literature, online databases and field sampling data. The model predicted potential suitable areas for R. indica in northern Colombia, central and northern Venezuela, Guyana, Suriname, east French Guiana and many parts of Brazil, including Roraima, the eastern Amazonas, northern Pará, Amapá and the coastal zones, from Pará to north of Rio de Janeiro. These results indicate the potential for significant R. indica related economic and social impacts in all of these countries, particularly in Brazil, because the suitable habitat regions overlap with agricultural areas for R. indica host plants such as coconuts and bananas.     

Does Fire Trigger Seed Germination in the Neotropical Savannas? Experimental Tests with Six Cerrado Species

The Cerrado (Brazilian savanna) is a biodiversity hotspot with a history of fire that goes back as far as 10 million years. Fire has influenced the evolution of several aspects of the vegetation, including reproduction and life cycles. This study tested how fire by‐products such as heat and smoke affect the germination of six species common to two Cerrado open physiognomies: wet grasslands and the campo sujo (grassland with scattered shrubs and dwarf trees). We subjected seeds collected in northern Brazil to heat shock and smoke treatments, both separately and combined, using different temperatures, exposure times, and smoke concentrations in aqueous solutions. High temperatures and smoke did not break seed dormancy nor stimulate germination of the Cerrado study species. However, seeds were not killed by high temperatures, indicating that they are fire‐tolerant. Our findings differed from those of other fire‐prone ecosystems (mostly of Mediterranean vegetation), where fire stimulates germination. Moreover, we provide important information regarding germination strategies of non‐woody Cerrado plants, showing the importance of considering the tolerance of seeds to high temperatures when evaluating fire‐related traits in fire‐prone ecosystems.     

Current distribution,breeding population and habitat use of the globally threatened Grey-necked Picathartes Picathartes oreas in south-eastern Nigeria: a call for conservation action

The Grey-necked Picathartes Picathartes oreas is a globally threatened bird species in Africa with a wild population of less than 10,000 individuals. The Nigerian population, which has been poorly studied, is restricted to the forest of Cross River. This study re-assessed the distribution, breeding population, habitat use and current threats of the Grey-necked Picathartes by revisiting the 91 breeding sites identified during the first and only survey of the species in 1987. We estimated a breeding population of 164 individuals across 82 breeding sites. Only 72 breeding sites were found in the localities where 91 had been registered in 1987. Thirteen (18%) of these 72 sites were no longer active and showed evidence of human disturbance. The occurrence of Grey-necked Picathartes’ nest sites was positively predicted by higher number of emergent trees, larger rocks and negatively related to disturbance matrices. Similarly, larger colony sizes were associated with high canopy cover and rock height. Also, the probability of finding an active nest within a breeding colony was significantly predicted by increased canopy, tree density and ground cover. Human threats included farming, wire snares, egg and juvenile removal, bush burning, and hunter’s camps. These threats, though specific to the Grey-necked Picathartes, threaten the integrity of the Cross River forest habitats.     

Assessment of chemical-crosslink-assisted protein structure modeling in CASP13

With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest-to-date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.     

Protein structure prediction assisted with sparse NMR data in CASP13

CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and ¹⁵N-¹H residual dipolar coupling data, typical of that obtained for ¹⁵N,¹³C-enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR-assisted prediction groups also did very well with these data. CASP13 also assessed whether incorporation of sparse NMR data improves the accuracy of protein structure prediction relative to nonassisted regular methods. In most cases, incorporation of sparse, noisy NMR data results in models with higher accuracy. The best NMR-assisted models were also compared with the best regular predictions of any CASP13 group for the same target. For six of 13 targets, the most accurate model provided by any NMR-assisted prediction group was more accurate than the most accurate model provided by any regular prediction group; however, for the remaining seven targets, one or more regular prediction method provided a more accurate model than even the best NMR-assisted model. These results suggest a novel approach for protein structure determination, in which advanced prediction methods are first used to generate structural models, and sparse NMR data is then used to validate and/or refine these models.     

Functional characterization of Ape1 variants identified in the human population

Apurinic/apyrimidinic (AP) sites are common mutagenic and cytotoxic DNA lesions. Ape1 is the major human repair enzyme for abasic sites and incises the phosphodiester backbone 5′ to the lesion to initiate a cascade of events aimed at removing the AP moiety and maintaining genetic integrity. Through resequencing of genomic DNA from 128 unrelated individuals, and searching published reports and sequence databases, seven amino acid substitution variants were identified in the repair domain of human Ape1. Functional characterization revealed that three of the variants, L104R, E126D and R237A, exhibited ~40–60% reductions in specific incision activity. A fourth variant, D283G, is similar to the previously characterized mutant D283A found to exhibit ~10% repair capacity. The most common substitution (D148E; observed at an allele frequency of 0.38) had no impact on endonuclease and DNA binding activities, nor did a G306A substitution. A G241R variant showed slightly enhanced endonuclease activity relative to wild-type. In total, four of seven substitutions in the repair domain of Ape1 imparted reduced function. These reduced function variants may represent low penetrance human polymorphisms that associate with increased disease susceptibility.     

Comparison of Free-Living Amoebae in Hot Water Systems of Hospitals with Isolates from Moist Sanitary Areas by Identifying Genera and Determining Temperature Tolerance

Legionella-contaminated hot water systems and moist sanitary areas in six hospitals were sampled for amoebae by following a standardized collection protocol. Genus identifications and temperature tolerance determinations were made. Amoebae identified as Hartmannella vermiformis (65%), Echinamoebae spp. (15%), Saccamoebae spp. (12%), and Vahlkampfia spp. (9%) were detected in 29 of 56 (52%) hot water samples. Twenty-three of 49 (47%) swabs obtained from moist areas were amoeba positive. The following genera were identified: Acanthamoeba (22%), Naegleria (22%), Vahlkampfia (20%), Hartmannella (15%), and Vanella (7%). The temperature tolerance of amoebae from hot water systems was strikingly different from that of amoebae from moist areas. At 44°C on agar, 59% of amoebic isolates sampled from hot water systems showed growth. The corresponding value for isolates from moist areas was only 17%. Six Acanthamoeba isolates from the moist areas were considered potential pathogens. Four Hartmannella and two Saccamoeba isolates from hot water could be cultured at 53°C.     

Ground use by northern muriquis (Brachyteles hypoxanthus)

Many arboreal primates descend to the ground, a custom that may occur more frequently in disturbed habitats, and in the presence of researchers to whom the primates are habituated. In this paper, we describe opportunistic observations of ground use in two groups of northern muriquis (Brachyteles hypoxanthus) at the RPPN Feliciano Miguel Abdala, Minas Gerais, Brazil. Members of both groups were observed drinking, resting, feeding, playing, and traveling on the ground to different degrees, and variation in the levels of habituation of the two groups may be responsible for the differences in the distribution of their terrestrial activities. The potential increase in vulnerability to predation or disease owing to ground use has implications for the conservation of this critically endangered species.