Diagrammatic Scales for Assessing Brown Eye Spot (Cercospora coffeicola) in Red and Yellow Coffee Cherries

Brazil is the world's largest coffee producer. Brown eye spot (BES) (Cercospora coffeicola) is a major crop disease that can cause 15–30% production losses and decrease the coffee beverage quality. Although the influence of this disease on beverage quality has been studied, diagrammatic scales for assessment of the disease severity in berries are still unexplored. Thus, this study has developed and validated diagrammatic scales to assess the severity of BES. Two diagrammatic scales were designed to assess the disease in berries, which can be yellow or red depending on the cultivar. The scale of yellow berries had nine grades: grade 0: 0%; 1: 0.1–5.0%; 2: 5.1–10.0%; 3: 10.1–15.0%; 4: 15.1–20.0%; 5: 20.1–30.0%; 6: 30.1–40.0%; 7: 40.1–60.0%; and 8: higher than 60.0%, while the scale of red berries had eight grades: grade 0: 0%; 1: 0.1–2.5%; 2: 2.6–5.0%; 3: 5.1–10.0%; 4: 10.1–20.0%; 5: 20.1–30.0%; 6: 30.1–50.0%; and 7: higher than 50.0% severity. Using scales improved accuracy and precision with R² = 0.99 and provided good repeatability and reproducibility of assessments of disease severity. Both scales can be used because the different berry colour influenced the accuracy and precision between the scales.     

Genomic variation at the tips of the adaptive radiation of Darwin's finches

Adaptive radiation unfolds as selection acts on the genetic variation underlying functional traits. The nature of this variation can be revealed by studying the tips of an ongoing adaptive radiation. We studied genomic variation at the tips of the Darwin's finch radiation; specifically focusing on polymorphism within, and variation among, three sympatric species of the genus Geospiza. Using restriction site‐associated DNA (RAD‐seq), we characterized 32 569 single‐nucleotide polymorphisms (SNPs), from which 11 outlier SNPs for beak and body size were uncovered by a genomewide association study (GWAS). Principal component analysis revealed that these 11 SNPs formed four statistically linked groups. Stepwise regression then revealed that the first PC score, which included 6 of the 11 top SNPs, explained over 80% of the variation in beak size, suggesting that selection on these traits influences multiple correlated loci. The two SNPs most strongly associated with beak size were near genes associated with beak morphology across deeper branches of the radiation: delta‐like 1 homologue (DLK1) and high‐mobility group AT‐hook 2 (HMGA2). Our results suggest that (i) key adaptive traits are associated with a small fraction of the genome (11 of 32 569 SNPs), (ii) SNPs linked to the candidate genes are dispersed throughout the genome (on several chromosomes), and (iii) micro‐ and macro‐evolutionary variation (roots and tips of the radiation) involve some shared and some unique genomic regions.     

PbsP,a cell wall‐anchored protein that binds plasminogen to promote hematogenous dissemination of group B Streptococcus

Streptococcus agalactiae (Group B Streptococcus or GBS) is a leading cause of invasive infections in neonates whose virulence is dependent on its ability to interact with cells and host components. We here characterized a surface protein with a critical function in GBS pathophysiology. This adhesin, designated PbsP, possesses two Streptococcal Surface Repeat domains, a methionine and lysine‐rich region, and a LPXTG cell wall‐anchoring motif. PbsP mediates plasminogen (Plg) binding both in vitro and in vivo and we showed that cell surface‐bound Plg can be activated into plasmin by tissue plasminogen activator to increase the bacterial extracellular proteolytic activity. Absence of PbsP results in a decreased bacterial transmigration across brain endothelial cells and impaired virulence in a murine model of infection. PbsP is conserved among the main GBS lineages and is a major plasminogen adhesin in non‐CC17 GBS strains. Importantly, immunization of mice with recombinant PbsP confers protective immunity. Our results indicate that GBS have evolved different strategies to recruit Plg which indicates that the ability to acquire cell surface proteolytic activity is essential for the invasiveness of this bacterium.     

Pathology Tissue-quantitative Mass Spectrometry Analysis to Profile Histone Post-translational Modification Patterns in Patient Samples

Histone post-translational modifications (hPTMs) generate a complex combinatorial code that has been implicated with various pathologies, including cancer. Dissecting such a code in physiological and diseased states may be exploited for epigenetic biomarker discovery, but hPTM analysis in clinical samples has been hindered by technical limitations. Here, we developed a method (PAThology tissue analysis of Histones by Mass Spectrometry - PAT-H-MS) that allows to perform a comprehensive, unbiased and quantitative MS-analysis of hPTM patterns on formalin-fixed paraffin-embedded (FFPE) samples. In pairwise comparisons, histone extracted from formalin-fixed paraffin-embedded tissues showed patterns similar to fresh frozen samples for 24 differentially modified peptides from histone H3. In addition, when coupled with a histone-focused version of the super-SILAC approach, this method allows the accurate quantification of modification changes among breast cancer patient samples. As an initial application of the PAThology tissue analysis of Histones by Mass Spectrometry method, we analyzed breast cancer samples, revealing significant changes in histone H3 methylation patterns among Luminal A-like and Triple Negative disease subtypes. These results pave the way for retrospective epigenetic studies that combine the power of MS-based hPTM analysis with the extensive clinical information associated with formalin-fixed paraffin-embedded archives.Histone post-translational modifications (hPTMs)¹ generate a complex combinatorial code that plays a critical role during the physiological and pathological regulation of gene expression (1). Alterations in histone modification patterns have been linked with various diseases, including cancer, often as a result of the aberrant expression or localization of histone modifying enzymes (2). Therefore, accurately dissecting hPTM patterns in normal and diseased tissues could yield epigenetic biomarkers useful for prognostic, diagnostic, and therapeutic purposes. Immunohistochemistry studies have shown the potential of this strategy (3, 4), but they were limited to the analysis of only a few hPTMs. In addition, despite their sensitivity and ease of use, antibody-based assays are hindered by issues such as the difficulty in detecting adjacent modifications and the limited linearity of the signal. As an alternative to traditional antibody-based methods, in recent years MS has become the elective method to analyze hPTMs, thanks to its unbiased nature, accuracy and its ability to quantitate modifications and detect their combinations. Various MS-based workflows optimized for hPTM analysis have been developed (5), but most of the studies focused on cell lines and animal tissue, whereas the potential offered by the analysis of clinical samples has been left largely unexploited. In particular, the MS-based analysis of hPTMs from formalin-fixed paraffin-embedded (FFPE) samples has never been addressed.Paraffin embedding following fixation in buffered formalin is the storage method of choice for clinical specimens, thus representing an invaluable source of clinical samples linked to retrospective patient information. Large formalin-fixed paraffin embedded (FFPE) archives, which are available in many hospitals, have been successfully exploited for DNA and RNA analyses, including chromatin immunoprecipitation (6, 7). However, the extensive protein cross-linking generated by formaldehyde fixation has hindered the proteomic study of this type of tissue. This problem has been addressed and overcome only recently in global proteomic studies by taking advantage of extraction protocols based on heat-induced antigen retrieval techniques derived from immunohistochemistry (8, 9). Moreover, a few studies showed the possibility to globally analyze protein post-translational modifications, such as glycosylation and phosphorylation, from fixed and embedded tissues (10–12).Here, we report for the first time the successful application of MS-based analysis of hPTMs to human clinical samples, focusing in particular on the development and validation of a method (PAT-H-MS) to extract histones from FFPE tissues in yield and purity sufficient to enable the subsequent use of a proteomic workflow optimized for hPTM analysis (13). By using this method we were able to profile in a quantitative manner 24 distinct modified histone peptides from human FFPE breast cancer samples belonging to different subtypes, identifying differences in histone methylation patterns of potential clinical relevance. Thus, PAT-H-MS represents a valid approach for hPTM analysis of clinical samples.     

Beta‐amyloid 1‐42 monomers,but not oligomers,produce PHF‐like conformation of Tau protein

The mechanistic relationship between amyloid β1‐42 (Aβ1‐42) and the alteration of Tau protein are debated. We investigated the effect of Aβ1‐42 monomers and oligomers on Tau, using mice expressing wild‐type human Tau that do not spontaneously develop Tau pathology. After intraventricular injection of Aβ1‐42, mice were sacrificed after 3 h or 4 days. The short‐lasting treatment with Aβ monomers, but not oligomers, showed a conformational PHF‐like change of Tau, together with hyperphosphorylation. The same treatment induced increase in concentration of GSK3 and MAP kinases. The inhibition of the kinases rescued the Tau changes. Aβ monomers increased the levels of total Tau, through the inhibition of proteasomal degradation. Aβ oligomers reproduced all the aforementioned alterations only after 4 days of treatment. It is known that Aβ1‐42 monomers foster synaptic activity. Our results suggest that Aβ monomers physiologically favor Tau activity and dendritic sprouting, whereas their excess causes Tau pathology. Moreover, our study indicates that anti‐Aβ therapies should be targeted to Aβ1‐42 monomers too.     

Skin microbiota of first cousins affected by psoriasis and atopic dermatitis

Background

Psoriasis and atopic dermatitis (AD) are chronic inflammatory skin diseases, which negatively influence the quality of life. In the last years, several evidences highlighted the pivotal role of skin bacteria in worsening the symptomatology of AD and psoriasis. In the present study we evaluated the skin microbiota composition in accurately selected subjects affected by (AD) and psoriasis.

Methods

Three first cousins were chosen for the study according to strict selection of criteria. One subject was affected by moderate AD, one had psoriasis and the last one was included as healthy control. Two lesional skin samples and two non-lesional skin samples (for AD and psoriatic subjects) from an area of 2 cm² behind the left ear were withdrawn by mean of a curette. For the healthy control, two skin samples from an area of 2 cm² behind the left ear were withdrawn by mean of a curette. DNA was extracted and sequencing was completed on the Ion Torrent PGM platform. Culturing of Staphylococcus aureus from skin samples was also performed.

Results

The psoriatic subject showed a decrease in Firmicutes abundance and an increase in Proteobacteria abundance. Moreover, an increase in Streptococcaceae, Rhodobacteraceae, Campylobacteraceae and Moraxellaceae has been observed in psoriatic subject, if compared with AD individual and control. Finally, AD individual showed a larger abundance of S. aureus than psoriatic and healthy subjects. Moreover, the microbiota composition of non-lesional skin samples belonging to AD and psoriatic individuals was very similar to the bacterial composition of skin sample belonging to the healthy control.

Conclusion

Significant differences between the skin microbiota of psoriatic individual and healthy and AD subjects were observed.