Time-series reconstruction of the molecular architecture of human centriole assembly.

Centriole biogenesis, as in most organelle assemblies, involves the sequential recruitment of sub-structural elements that will support its function. To uncover this process, we correlated the spatial location of 24 centriolar proteins with structural features using expansion microscopy. A time-series reconstruction of protein distributions throughout human procentriole assembly unveiled the molecular architecture of the centriole biogenesis steps. We found that the process initiates with the formation of a naked cartwheel devoid of microtubules. Next, the bloom phase progresses with microtubule blade assembly, concomitantly with radial separation and rapid cartwheel growth. In the subsequent elongation phase, the tubulin backbone grows linearly with the recruitment of the A-C linker, followed by proteins of the inner scaffold (IS). By following six structural modules, we modeled 4D assembly of the human centriole. Collectively, this work provides a framework to investigate the spatial and temporal assembly of large macromolecules.

Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide.

We report detailed peptide-binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV-1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide-binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV-1. Among the strong HLA binders (IC50 ≤ 50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA-A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV-1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions. In particular, Indigenous peoples of America show both higher frequencies of strongest and lower frequencies of weakest HLA binders. As many HLA proteins are found to be strong binders of peptides derived from distinct viral families, and are hence promiscuous (or generalist), we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to past pathogenic infections. Our findings are highly relevant for both evolutionary genetics and the development of vaccine therapies. However they should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables.

How the environmental fate of clomazone in rice fields is influenced by amendment with olive-mill waste under different regimes of irrigation and tillage.

BACKGROUND: Irrigation and tillage systems alone or in combination with organic amendments can strongly influence soil properties, which in turn may also modify the environmental fate of any pesticides applied. This study was aimed at determining how amendment with composted olive-mill waste (W) influenced leaching, sorption, and persistence of the herbicide clomazone in rice field soils under different tillage and irrigation management practices. The field trial conducted covered 3 years in succession, with six treatments: irrigation by sprinkler and conventional tillage without (ST) or with W application (80 Mg ha-1 ) (STW), irrigation by sprinkler but no tillage (SNT), irrigation by sprinkler but no tillage with W application (SNTW), and continuous flooding irrigation and tillage without (FT) and with W application (FTW). RESULTS: Application of W significantly increased the adsorption of clomazone to soil in the first and third years. In the first year, the persistence of clomazone under aerobic (t1/2  = 33.1-36.3 days) and anaerobic incubation conditions (t1/2  = 3.43-10.8 days) decreased after W application to t1/2 values in the ranges 18.1-29.7 and 3.06-5.44 days, respectively. However, in the third year, although clomazone persistence increased significantly in SNT and ST when W was applied under both incubation conditions, it decreased significantly in FT management under anaerobic incubation conditions. The addition of W led to less leaching of clomazone, particularly for the FT case where the herbicide leaching losses were 2.8 and 2.6 times lower in the first and third years after W addition, respectively. CONCLUSIONS: Using W as an organic amendment could be regarded as an invaluable strategy to reduce water contamination by clomazone in rice production, especially under traditional tillage and flooding management. © 2019 Society of Chemical Industry.

Environmental drivers of rhodolith beds and epiphytes community along the South Western Atlantic coast.

Environmental conditions shape the occurrence and abundance of habitat-building organisms at global scales. Rhodolith beds structure important hard substrate habitats for a large number of marine benthic organisms. These organisms can benefit local biodiversity levels, but also compete with rhodoliths for essential resources. Therefore, understanding the factors shaping the distribution of rhodoliths and their associated communities along entire distributional ranges is of much relevance for conservational biology, particularly in the scope of future environmental changes. Here we predict suitable habitat areas and identify the main environmental drivers of rhodoliths' variability and of associated epiphytes along a large-scale latitudinal gradient. Occurrence and abundance data were collected throughout the South-western Atlantic coast (SWA) and modelled against high resolution environmental predictors extracted from Bio-Oracle. The main drivers for rhodolith occurrence were light availability and temperature at the bottom of the ocean, while abundance was explained by nitrate, temperature and current velocity. Tropical regions showed the highest abundance of rhodoliths. No latitudinal pattern was detected in the variability of epiphytes abundance. However, significant differences were found between sampled sites regarding the composition of predominant taxa. The predictors influencing such differences were temperature and nitrate. The Tropical region is abundant in species with warm-water affinities, decreasing toward warm temperate region. The expressive occurrence of tropical species not referred before for warm temperate beds indicate a plausible tropicalization event.

Metagenomic Analysis of Cyanobacteria in an Oligotrophic Tropical Estuary, South Atlantic.

This study assessed the species composition, distribution, and functional profiles of cyanobacteria in Camamu Bay, a tropical oligotrophic estuarine system on the northeast coast of Brazil, using shotgun metagenomic sequencing. Surface-water samples were evaluated in two different rainfall periods (rainy and dry seasons), at nine stations in the three hydrodynamic regions of the bay. At a fixed sampling station, on each season, samples were taken over a tidal cycle at 3-h intervals over 12 h. A total of 219 cyanobacterial taxa were identified, demonstrating a diverse community of freshwater, euryhaline, and marine cyanobacteria. The genera of greater relative abundance, Synechococcus and Prochlorococcus, corresponded to the picoplankton fraction. Although Camamu Bay has conspicuous marine characteristics, the contribution of freshwater during the rainy season caused variation in cyanobacteria community, with an increase in species richness. Due the high prevalence of Synechococcus (90% of the sequences), the functional analysis revealed only minor differences in gene content between the dry and rainy seasons. In both rainy and dry seasons, an increase in Prochlorococcus relative abundance occurred during high tide, demonstrating the tidal influence in the bay. The environmental characteristics of the bay provide niche conditions for a wide variety of cyanobacteria, including freshwater, euryhaline, and marine strains.

The influence of environmental features in the content of mycosporine-like amino acids in red marine algae along the Brazilian coast.

Mycosporine-like amino acids (MAA) are ultraviolet screen substances synthesized by marine algae. The physiological function of these substances is related to cellular protection against UV radiation and as a protective mechanism against oxidative stress. These substances can be found mainly in the ocean, among red seaweeds. Its concentration in organisms has been related to ultraviolet radiation and availability of inorganic nitrogen in the environment. We start our study of MAA content in different species to understand if environmental conditions influence the concentration of MAAs in red seaweeds. The Brazilian coast presents abiotic factors that interact to create different physical-chemical features in the environment. We collected 441 samples from 39 species of red seaweed easily found in the intertidal zone, in low tide, during the summer of 2015. The sampling encompassed a latitudinal gradient (3° S to 28°5' S) at 23 points along the coast. We quantified and identified the content of MAAs in species through the method of high performance liquid chromatography. We detected for the first time the occurrence of MAAs in certain species of red algae that have not been reported to contain MAAs before. We confirmed that some environmental factors influenced the content of MAAs. Enhanced MAA contents, for example, were found in environments with a basic pH, a high ultraviolet index, and high concentrations of phosphate and nitrate. Salinity, dissolved oxygen and variations of sea surface temperature also influenced, in a secondary way, MAA content in algae in their natural environments.

Correction to: "Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection".

[This corrects the article DOI: 10.4137/EBO.S33488.].

Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection.

SELECTOR is a software package for studying the evolution of multiallelic genes under balancing or positive selection while simulating complex evolutionary scenarios that integrate demographic growth and migration in a spatially explicit population framework. Parameters can be varied both in space and time to account for geographical, environmental, and cultural heterogeneity. SELECTOR can be used within an approximate Bayesian computation estimation framework. We first describe the principles of SELECTOR and validate the algorithms by comparing its outputs for simple models with theoretical expectations. Then, we show how it can be used to investigate genetic differentiation of loci under balancing selection in interconnected demes with spatially heterogeneous gene flow. We identify situations in which balancing selection reduces genetic differentiation between population groups compared with neutrality and explain conflicting outcomes observed for human leukocyte antigen loci. These results and three previously published applications demonstrate that SELECTOR is efficient and robust for building insight into human settlement history and evolution.

The distribution of MICA alleles in an Austrian population: evidence for increasing polymorphism.

The Major Histocompatibility Complex Class I Chain-Related Gene A (MICA) is located 46.4 Kb centromeric to HLA-B locus on chromosome 6; 84 alleles have been described so far. To assess the distribution of MICA alleles in an Austrian population, 322 unrelated Austrian blood donors have been typed for MICA by direct sequencing of amplified exons 2-5; sequencing of exon 6 and separating alleles by haplotype specific primers or by cloning was performed to resolve ambiguities. HLA-B was typed at low level resolution and linkage disequilibrium was determined. We observed 20 already known and four novel MICA alleles. MICA*008:01/04 was the most frequent allele (42%), followed by MICA*002:01 (11%) and MICA*009:01 (9%), three alleles (MICA*029, *067 and *068) were observed only once. No deviation from the Hardy Weinberg equilibrium was observed. Linkage disequilibrium between MICA and HLA-B alleles was observed, most extensively between MICA*008:01/04 and HLA-B*07. Our population data are in agreement with other European populations. The fact that four novel alleles have been observed indicates that the polymorphism of MICA is larger than currently estimated.

Haplotype diversity generated by ancient recombination-like events in the MHC of Indian rhesus macaques.

The Mamu-A, Mamu-B, and Mamu-DRB genes of the rhesus macaque show several levels of complexity such as allelic heterogeneity (polymorphism), copy number variation, differential segregation of genes/alleles present on a haplotype (diversity) and transcription level differences. A combination of techniques was implemented to screen a large panel of pedigreed Indian rhesus macaques (1,384 individuals representing the offspring of 137 founding animals) for haplotype diversity in an efficient and inexpensive manner. This approach allowed the definition of 140 haplotypes that display a relatively low degree of region variation as reflected by the presence of only 17 A, 18 B and 22 DRB types, respectively, exhibiting a global linkage disequilibrium comparable to that in humans. This finding contrasts with the situation observed in rhesus macaques from other geographic origins and in cynomolgus monkeys from Indonesia. In these latter populations, nearly every haplotype appears to be characterised by a unique A, B and DRB region. In the Indian population, however, a reshuffling of existing segments generated "new" haplotypes. Since the recombination frequency within the core MHC of the Indian rhesus macaques is relatively low, the various haplotypes were most probably produced by recombination events that accumulated over a long evolutionary time span. This idea is in accord with the notion that Indian rhesus macaques experienced a severe reduction in population during the Pleistocene due to a bottleneck caused by geographic changes. Thus, recombination-like processes appear to be a way to expand a diminished genetic repertoire in an isolated and relatively small founder population.

"Detachment of the carinal hook following endobronchial intubation with a double lumen tube".

BACKGROUND: Carinal hooks increases difficulty at endotracheal intubation. Amputation of the carinal hook during passage and malpositioning of the tube to the hook are some of the potential problems related with left-sided Carlens double lumen tube (DLT). This article reports an amputation of the hook during a difficult selective intubation and aimed at calling the attention to complications associated with DLTs and the importance of fiberoptic bronchoscopy. CASE PRESENTATION: A 68 year-old woman was scheduled for right-sided thoracotomy in whom blind DLT insertion was performed. Narrowed trachea causes difficulty in rotating the DLT 90° counter-clockwise. After carinal hook was noticed upon visual inspection of the DLT, fiberoptic bronchoscopy was used to remove the missing part (with the use of forceps) from the right mainstem bronchus. CONCLUSION: Insertion of DLTs with carinal hook is associated with technical problems and potentially life-threatening hazards have discouraged their use. Fiberoptic evaluation and repositioning solves most of the problems. Although amputation of the carinal hook has not been previously reported, clinicians should be alert. This case report emphasizes the utility of the fiberoptic bronchoscopy in the operating theatre for placement, positioning and inspection of the carinal hook DLT.

Tools for analysing ambiguous HLA data.

Analyses of large projects involving human leukocyte antigen data often face the difficulty of having data sets gathered using distinct techniques and resolution levels. Furthermore, it is not infrequent that missing and ambiguous data arise at one or several loci. This article describes a set of computer programs that can be used to work efficiently with these kinds of data. The tasks of concern include format conversions, data recoding and replacement, and Expectation-Maximization (gene-counting) based frequency estimation for sets with ambiguous cases either under the assumption of Hardy-Weinberg equilibrium frequencies or when some deviation exists (measured by a one degree of freedom inbreeding coefficient). This set of utilities is built on the top of a data format formally defined. The formal definition of the format allows to express all kinds of observable ambiguities, to define a simpler form for writing and manipulating data set files and to make substantial modifications of the actual symbols chosen to describe the data.

Association of HLA DQ4-DR8 haplotype with papillary thyroid carcinomas.

OBJECTIVE: The association of the human leucocyte antigen (HLA) system with thyroid carcinomas is not clear. We sought to relate HLA alleles to susceptibility to papillary thyroid carcinoma (PTC) and also to clinical and pathological characteristics of PTC patients. DESIGN AND PATIENTS: The distribution of HLA in 181 unrelated Caucasian patients with PTC was compared to the HLA distribution in 315 normal controls, 31 patients with follicular carcinoma (FTC), 29 patients with lymphocytic thyroiditis (LT) and 50 patients with multinodular goitre (MNG), using a microlymphocytotoxicity assay. RESULTS: Compared to normal controls, patients with PTC showed a significantly increased frequency of HLA-DQ4 [12.8%vs. 3.5%, P=0.0005, P(corrected) (P(c))=0.0032, odds ratio (OR)=4.058, 95% confidence interval (95% CI)=1.820-9.045] and HLA-DR8 (10.9%vs. 4.3%, P=0.013, P(c) > 0.05, OR=2.752, 95% CI=1.275-5.940). DQ4 and DR8 were also significantly increased in patients with MNG (DQ4, 16.3%; DR8, 16.3%) compared to controls (DQ4, P=0.0019, P(c)=0.011, OR=5.420, 95% CI=1.978-14.852; DR8, P=0.0044, P(c)=0.062). Linkage disequilibrium (LD) for these two alleles was present in controls (D=0.0130, P=9.7e-57) and in MNG patients (D=0.0730, P=4.6e-19) but not in PTC patients (D=0.038, P>0.05). In the subgroup of PTC subjects with concomitant 0thyroidal neoplasias (n=27), there was a significant (P< 0.05) increase in the frequency of B57 (18.5%), DR11 (56.5%) and DQ3 (81.8%) compared to PTC patients without coexistent neoplasias (2.0%, 21% and 47%, respectively). No significant differences of HLA allele distribution was found in relation to PTC histology, age at diagnosis (> 45 or