Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny,Physiology, and Niche Adaptation on Human Skin

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin’s carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin.     

Discovery of genomic regions and candidate genes controlling shelling percentage using QTL‐seq approach in cultivated peanut (Arachis hypogaea L.)

Cultivated peanut (Arachis hypogaea L.) is an important grain legume providing high‐quality cooking oil, rich proteins and other nutrients. Shelling percentage (SP) is the 2nd most important agronomic trait after pod yield and this trait significantly affects the economic value of peanut in the market. Deployment of diagnostic markers through genomics‐assisted breeding (GAB) can accelerate the process of developing improved varieties with enhanced SP. In this context, we deployed the QTL‐seq approach to identify genomic regions and candidate genes controlling SP in a recombinant inbred line population (Yuanza 9102 × Xuzhou 68‐4). Four libraries (two parents and two extreme bulks) were constructed and sequenced, generating 456.89–790.32 million reads and achieving 91.85%–93.18% genome coverage and 14.04–21.37 mean read depth. Comprehensive analysis of two sets of data (Yuanza 9102/two bulks and Xuzhou 68‐4/two bulks) using the QTL‐seq pipeline resulted in discovery of two overlapped genomic regions (2.75 Mb on A09 and 1.1 Mb on B02). Nine candidate genes affected by 10 SNPs with non‐synonymous effects or in UTRs were identified in these regions for SP. Cost‐effective KASP (Kompetitive Allele‐Specific PCR) markers were developed for one SNP from A09 and three SNPs from B02 chromosome. Genotyping of the mapping population with these newly developed KASP markers confirmed the major control and stable expressions of these genomic regions across five environments. The identified candidate genomic regions and genes for SP further provide opportunity for gene cloning and deployment of diagnostic markers in molecular breeding for achieving high SP in improved varieties.     

Estimation of genetic parameters for disease‐resistance traits in Cynoglossus semilaevis (Günther, 1873)

The objective of this study was to estimate genetic parameters for three traits based on 28 Cynoglossus semilaevis families approximately 6 months of age (at least 5 cm total length), including trait_1 (survival of 26 families, 3434 individuals in total subjected to challenge tests with Edwardsiella tarda), trait_2 (survival of 20 families, 2016 individuals in total subjected to challenge tests with Vibrio anguillarum) and trait_3 (survival of 27 families, 9340 individuals tagged at circa 180 days of age and reared in indoor ponds for circa another 5 months). The result showed that there were large differences in the survival of the families after challenge (11.11–65.31% for E. tarda and 9.18–70.54% for V. anguillarum). Additionally, the survival of families reared in indoor ponds was also different, varying from 21.00% to 73.67%. Heritabilities of the three traits varied from 0.14 to 0.26, as estimated by the linear model (LM) and the threshold model (TM). The trait_1 heritabilities (0.26 and 0.19 estimated by LM and TM) were higher than those of the others (0.20 and 0.23 estimated by LM, 0.14 and 0.19 estimated by TM). The estimates of heritabilities using LM were consistently higher than those of TM in this study. There were significant medium genetic correlations of 0.44 and 0.42 between trait_1 and trait_2 obtained from LM and TM (P < 0.05). However, very low and non‐significant genetic correlations of trait_1 and trait_3 (?0.10 for LM, ?0.05 for TM), as well as those of trait_2 and trait_3 (0.05 for LM, 0.04 for TM) were obtained. Therefore, indirect selection for trait_1 and trait_2 was effective, but almost ineffectual for trait_1 and trait_3 as well as trait_2 and trait_3. Otherwise, there was no significant difference in the predictive abilities of LM and TM. Two families resistant to both Edwardsiella tarda and Vibrio anguillarum were selected plus one family resistant to both Vibrio anguillarum and naturally infected by unknown pathogens through family selection. As there was very low and non‐significant genetic correlation of trait_3 and trait_1 as well as trait_2, superior strains are anticipated with the ability to resist two or more kinds of diseases, through the crossing of families selected for the three traits described above. The results support the hypothesis that genetic variation exists for disease survival, which could be used to design a breeding program for selecting strains of Cynoglossus semilaevis with high disease resistance.     

Retinoid X Receptor Agonists Upregulate Genes Responsible for the Biosynthesis of All-Trans-Retinoic Acid in Human Epidermis

UAB30 is an RXR selective agonist that has been shown to have potential cancer chemopreventive properties. Due to high efficacy and low toxicity, it is currently being evaluated in human Phase I clinical trials by the National Cancer Institute. While UAB30 shows promise as a low toxicity chemopreventive drug, the mechanism of its action is not well understood. In this study, we investigated the effects of UAB30 on gene expression in human organotypic skin raft cultures and mouse epidermis. The results of this study indicate that treatment with UAB30 results in upregulation of genes responsible for the uptake and metabolism of all-trans-retinol to all-trans-retinoic acid (ATRA), the natural agonist of RAR nuclear receptors. Consistent with the increased expression of these genes, the steady-state levels of ATRA are elevated in human skin rafts. In ultraviolet B (UVB) irradiated mouse skin, the expression of ATRA target genes is found to be reduced. A reduced expression of ATRA sensitive genes is also observed in epidermis of mouse models of UVB-induced squamous cell carcinoma and basal cell carcinomas. However, treatment of mouse skin with UAB30 prior to UVB irradiation prevents the UVB-induced decrease in expression of some of the ATRA-responsive genes. Considering its positive effects on ATRA signaling in the epidermis and its low toxicity, UAB30 could be used as a chemoprophylactic agent in the treatment of non-melanoma skin cancer, particularly in organ transplant recipients and other high risk populations.     

Construction of photodynamic‐effect immunofluorescence probes by a complex of quantum dots,immunoglobulin G and chlorin e6 and their application in HepG2 cell killing

In this study, tri‐functional immunofluorescent probes (Ce6–IgG–QDs) based on covalent combinations of quantum dots (QDs), immunoglobulin G (IgG) and chlorin e6 (Ce6) were developed and their photodynamic ability to induce the death of cancer cells was demonstrated. Strategically, one type of second‐generation photosensitizer, Ce6, was first coupled with anti‐IgG antibody using the EDC/NHS cross‐linking method to construct the photosensitive immunoconjugate Ce6–IgG. Then, a complex of Ce6–IgG–QDs immunofluorescent probes was obtained in succession by covalently coupling Ce6–IgG to water soluble CdTe QDs. The as‐manufactured Ce6–IgG–QDs maintained the bio‐activities of both the antigen–antibody‐based tumour targeting effects of IgG and the photodynamic‐related anticancer activities of Ce6. By way of polyclonal antibody interaction with rabbit anti‐human epidermal growth factor receptor (anti‐EGFR antibody, N‐terminus), Ce6–IgG–QDs were labelled indirectly onto the surface of human hepatocarcinoma (HepG2) cells in cell recognition and killing experiments. The results indicated that the Ce6–IgG–QDs probes have excellent tumour cell selectivity and higher photosensitivity in photodynamic therapy (PDT) compared with Ce6 alone, due to their antibody‐based specific recognition and location of HepG2 cells and the photodynamic effects of Ce6 killed cells based on efficient fluorescence resonance energy transfer between QDs and Ce6. Copyright © 2015 John Wiley & Sons, Ltd.     

Chalcone synthase homologous genes cloning and expression pattern in flowering <Emphasis Type="Italic">Fagopyrum tataricum</Emphasis> Gaertn

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is highly nutritious and an excellent dietary source of flavonoid compounds. Chalcone synthase (CHS) is the first key enzyme involved in flavonoid biosynthesis. Here, three putative CHS genes (designated as FtCHS1 (GU172165), FtCHS2 (KT284884), and FtCHS3 (KT284885) were isolated from tartary buckwheat. Nucleotide sequence analysis indicated that FtCHS1 and FtCHS2 each contained one intron of 444 bp and 157 bp, respectively. FtCHS3 included two introns, one of 86 bp and another of 73 bp. The results of quantitative real-time PCR (qRT-PCR) showed the FtCHSs expression presented the same pattern in the stems and flowers, with FtCHS1>FtCHS3>FtCHS2. A different tendency was found in leaves, with FtCHS3>FtCHS2>FtCHS1. However, there was no direct correlation between the three CHS expression and total flavonoids. Furthermore, high-performance liquid chromatography (HPLC) performance reveals rutin is the most abundant flavonoid in all tissues, leaves should be the main location for quercetin storage in tartary buckwheat.     

Photocatalytic antibacterial effects on TiO2-anatase upon UV-A and UV-A/VIS threshold irradiation

Photocatalysis mediated by the anatase modification of titanium dioxide (TiO₂) has shown antibacterial effects in medical applications. The aim of this study was to investigate the possibility of expanding the excitation wavelengths for photocatalytic antibacterial effects from ultraviolet (UV) into the visible light range. After deposition of salivary pellicle and adhesion of Streptococcus gordonii on anatase, different irradiation protocols were applied to induce photocatalysis: ultraviolet A (UV-A) > 320 nm; ultraviolet/visible (UV-A/VIS) light > 380 nm and > 390 nm; and VIS light 400–410 nm. A quartz crystal microbalance with dissipation (QCM-D) tests and microscopic examination were used to observe the photoinduced antibacterial effects. Salivary pellicle could be photocatalytically decomposed under all irradiation protocols. In contrast, effective photocatalytic attack of bacteria could be observed by UV-A as well as by UV-A/VIS at 380 nm < λ < 390 nm only. Wavelengths above 380 nm show promise for in situ therapeutic antifouling applications.     

Integrated analysis of clinical significance and functional involvement of microRNAs in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most common lethal cancers worldwide. To explore the potential prognosis-associated microRNAs (miRNAs) for HCC patients, we performed integrated analyses on the miRNA expression profiles from The Cancer Genome Atlas project. Genome-wide overall survival (OS)- and progression-free survival (PFS)-associated miRNA screening were performed by multivariate Cox proportional hazards regression analyses. A five-miRNA expression signature (miR-148a, miR-3677-3p, miR-744*, miR-210, and miR-3613-5p) was identified as an indicator for HCC OS (p < .0001; hazard ratio [HR] = 2.631). In addition, a seven-miRNA expression signature (miR-127-5p, miR-146a, miR-152, miR-193a-3p, miR-331-5p, miR-500a*, and miR-550a*) was identified as a predictor for HCC PFS (p < .0001; HR = 2.608). This systematic analysis suggested that both the OS- and PFS-associated signatures have better performance in HCC survival prediction than the conventional clinicopathological parameters. Further functional enrichment analysis of the corresponding genes targeted by these signature miRNAs revealed their biological significance in the PI3K-Akt signaling pathway. In conclusion, our present study identified a five-miRNA OS-associated signature and a seven-miRNA PFS-associated signature as HCC prognostic biomarkers with potential clinical significance, which could enable the development of novel targeted therapeutic strategies for HCC treatment.     

Sequential and compartmentalized action of Rabs,SNAREs, and MAL in the apical delivery of fusiform vesicles in urothelial umbrella cells

Uroplakins (UPs) are major differentiation products of urothelial umbrella cells and play important roles in forming the permeability barrier and in the expansion/stabilization of the apical membrane. Further, UPIa serves as a uropathogenic Escherichia coli receptor. Although it is understood that UPs are delivered to the apical membrane via fusiform vesicles (FVs), the mechanisms that regulate this exocytic pathway remain poorly understood. Immunomicroscopy of normal and mutant mouse urothelia show that the UP-delivering FVs contained Rab8/11 and Rab27b/Slac2-a, which mediate apical transport along actin filaments. Subsequently a Rab27b/Slp2-a complex mediated FV–membrane anchorage before SNARE-mediated and MAL-facilitated apical fusion. We also show that keratin 20 (K20), which forms a chicken-wire network ∼200 nm below the apical membrane and has hole sizes allowing FV passage, defines a subapical compartment containing FVs primed and strategically located for fusion. Finally, we show that Rab8/11 and Rab27b function in the same pathway, Rab27b knockout leads to uroplakin and Slp2-a destabilization, and Rab27b works upstream from MAL. These data support a unifying model in which UP cargoes are targeted for apical insertion via sequential interactions with Rabs and their effectors, SNAREs and MAL, and in which K20 plays a key role in regulating vesicular trafficking.