Artificial night lighting is gaining attention as a new type of pollution;however, studies of its impacts are scarce. Fireflies provide good models to investigate its effects on nocturnal wildlife, since they depend o...Artificial night lighting is gaining attention as a new type of pollution;however, studies of its impacts are scarce. Fireflies provide good models to investigate its effects on nocturnal wildlife, since they depend on their bioluminescence for reproduction. This study investigated the impact of artificial illumination on firefly activity at the new campus of the Federal University of São Carlos (Sorocaba, Brazil). The flashing activity of different firefly species, especially Photinus sp1 (82% of all occurrences), was investigated during 3 years, before and after the installation of multi metal vapor spotlights. Quantitative and qualitative analysis, performed in transects at different distances from the artificial light sources, showed significant negative effects on Photinus sp1 occurrence. This study proposes fireflies as potential flagship species and bioindicators for artificial night lighting and for the first time quantifies its effects, providing subsidies for future conservationist legislations regarding photopollution.展开更多
Chitinases catalyze the hydrolysis of chitin, a linear homopolymer of β-(1,4)-linked N-acetylglucosamine. The broad range of applications of chitinolytic enzymes makes their identification and study very promising. M...Chitinases catalyze the hydrolysis of chitin, a linear homopolymer of β-(1,4)-linked N-acetylglucosamine. The broad range of applications of chitinolytic enzymes makes their identification and study very promising. Metagenomic approaches offer access to functional genes in uncultured representatives of the microbiota and hold great potential in the discovery of novel enzymes, but tools to extensively explore these data are still scarce. In this study, we develop a chitinase mining pipeline to facilitate the comprehensive search of these enzymes in environmental metagenomic databases and also to explore phylogenetic relationships among the retrieved sequences. In order to perform the analyses, UniprotKB fungal and bacterial chitinases sequences belonging to the glycoside hydrolases (GH) family-18, 19 and 20 were used to generate 15 reference datasets, which were then used to generate high quality seed alignments with the MAFFT program. Profile Hidden Markov Models (pHMMs) were built from each seed alignment using the hmmbuild program of HMMER v3.0 package. The best-hit sequences returned by hmmsearch against two environmental metagenomic databases (Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis—CAMERA and Integrated Microbial Genomes—IMG/M) were retrieved and further analyzed. The NJ trees generated for each chitinase dataset showed some variability in the catalytic domain region of the metagenomic sequences and revealed common sequence patterns among all the trees. The scanning of the retrieved metagenomic sequences for chitinase conserved domains/signatures using both the InterPro and the RPS-BLAST tools confirmed the efficacy and sensitivity of our pHMM-based approach in detecting putative chitinases sequences. These analyses provide insight into the potential reservoir of novel molecules in metagenomic databases while supporting the chitinase mining pipeline developed in this work. By using our chitinase mining pipeline, a larger number of previously unannotated metagenomic chitinase sequences can be classified, enabling further studies on these enzymes.展开更多
Psoriasis is a chronic, recurrent inflammatory cutaneous disease. Psoriasis patients alternate between periods of remission and periods of exacerbation of the disease. Usually, psoriasis severity is clinically evaluat...Psoriasis is a chronic, recurrent inflammatory cutaneous disease. Psoriasis patients alternate between periods of remission and periods of exacerbation of the disease. Usually, psoriasis severity is clinically evaluated using tools like Psoriasis Area and Severity Index that present some limitations and subjectivity. Clinicians select the therapy according to psoriasis severity, aiming that patients achieve longer remission periods and improve their quality of life. Biological markers for diagnosis and prognosis of psoriasis help to establish its severity and to monitor the therapeutic response; moreover, biomarkers of psoriasis assist clinicians in their therapeutic decision to treat psoriasis and to choose earlier and more adequate therapeutic strategies, avoiding or minimising worsening of psoriasis. With these markers, they would be able to monitor therapeutics, avoiding unnecessary therapeutic surcharge or changes to a more aggressive therapy. As any attempt to identify these biomarkers should be encouraged, in this review,we will debate published data concerning the proposal of biomarkers to evaluate severity and response to treatment of psoriasis vulgaris.展开更多
Cucumber mosaic virus (CMV) has the broadest host range, infecting more than 1300 species in more than 500 genera from over 100 botanical families. In ornamental plants, CMV can cause mosaic and distortion of leaves, ...Cucumber mosaic virus (CMV) has the broadest host range, infecting more than 1300 species in more than 500 genera from over 100 botanical families. In ornamental plants, CMV can cause mosaic and distortion of leaves, stunting, color break, and malformation of flowers. CMV coat protein (CP) sequences obtained from seven ornamental plants and other homologous sequences available in GenBank were compared, and phylogenetic relationships were established. Total RNA from virus-infected ornamental species were extracted, submitted to RT-PCR with specific primers, and amplicons obtained were sequenced. A nucleotide substitution model and phylogenetic analyses were carried out using the PAUP program. The seven sequences of CMV CP obtained showed similar identity percentages and close relationships with subgroup I isolates from other countries and hosts. CMV isolates from different regions of S?o Paulo state, Brazil (Salvia splendens, Catharanthus roseus, Nematanthus nervosus (=Hypocyrta nervosa), Impatiens walleriana, Eucharis grandiflora and Commelina sp.) formed a monophyletic group, indicating a possible common origin. It was found that when lily sequences of CMV only from different geographic regions were compared, Brazilian isolates shared the same common ancestor with those from Poland and Taiwan. Furthermore, this monophyletic group presented a quite basal position.展开更多
文摘Artificial night lighting is gaining attention as a new type of pollution;however, studies of its impacts are scarce. Fireflies provide good models to investigate its effects on nocturnal wildlife, since they depend on their bioluminescence for reproduction. This study investigated the impact of artificial illumination on firefly activity at the new campus of the Federal University of São Carlos (Sorocaba, Brazil). The flashing activity of different firefly species, especially Photinus sp1 (82% of all occurrences), was investigated during 3 years, before and after the installation of multi metal vapor spotlights. Quantitative and qualitative analysis, performed in transects at different distances from the artificial light sources, showed significant negative effects on Photinus sp1 occurrence. This study proposes fireflies as potential flagship species and bioindicators for artificial night lighting and for the first time quantifies its effects, providing subsidies for future conservationist legislations regarding photopollution.
文摘Chitinases catalyze the hydrolysis of chitin, a linear homopolymer of β-(1,4)-linked N-acetylglucosamine. The broad range of applications of chitinolytic enzymes makes their identification and study very promising. Metagenomic approaches offer access to functional genes in uncultured representatives of the microbiota and hold great potential in the discovery of novel enzymes, but tools to extensively explore these data are still scarce. In this study, we develop a chitinase mining pipeline to facilitate the comprehensive search of these enzymes in environmental metagenomic databases and also to explore phylogenetic relationships among the retrieved sequences. In order to perform the analyses, UniprotKB fungal and bacterial chitinases sequences belonging to the glycoside hydrolases (GH) family-18, 19 and 20 were used to generate 15 reference datasets, which were then used to generate high quality seed alignments with the MAFFT program. Profile Hidden Markov Models (pHMMs) were built from each seed alignment using the hmmbuild program of HMMER v3.0 package. The best-hit sequences returned by hmmsearch against two environmental metagenomic databases (Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis—CAMERA and Integrated Microbial Genomes—IMG/M) were retrieved and further analyzed. The NJ trees generated for each chitinase dataset showed some variability in the catalytic domain region of the metagenomic sequences and revealed common sequence patterns among all the trees. The scanning of the retrieved metagenomic sequences for chitinase conserved domains/signatures using both the InterPro and the RPS-BLAST tools confirmed the efficacy and sensitivity of our pHMM-based approach in detecting putative chitinases sequences. These analyses provide insight into the potential reservoir of novel molecules in metagenomic databases while supporting the chitinase mining pipeline developed in this work. By using our chitinase mining pipeline, a larger number of previously unannotated metagenomic chitinase sequences can be classified, enabling further studies on these enzymes.
文摘Psoriasis is a chronic, recurrent inflammatory cutaneous disease. Psoriasis patients alternate between periods of remission and periods of exacerbation of the disease. Usually, psoriasis severity is clinically evaluated using tools like Psoriasis Area and Severity Index that present some limitations and subjectivity. Clinicians select the therapy according to psoriasis severity, aiming that patients achieve longer remission periods and improve their quality of life. Biological markers for diagnosis and prognosis of psoriasis help to establish its severity and to monitor the therapeutic response; moreover, biomarkers of psoriasis assist clinicians in their therapeutic decision to treat psoriasis and to choose earlier and more adequate therapeutic strategies, avoiding or minimising worsening of psoriasis. With these markers, they would be able to monitor therapeutics, avoiding unnecessary therapeutic surcharge or changes to a more aggressive therapy. As any attempt to identify these biomarkers should be encouraged, in this review,we will debate published data concerning the proposal of biomarkers to evaluate severity and response to treatment of psoriasis vulgaris.
文摘Cucumber mosaic virus (CMV) has the broadest host range, infecting more than 1300 species in more than 500 genera from over 100 botanical families. In ornamental plants, CMV can cause mosaic and distortion of leaves, stunting, color break, and malformation of flowers. CMV coat protein (CP) sequences obtained from seven ornamental plants and other homologous sequences available in GenBank were compared, and phylogenetic relationships were established. Total RNA from virus-infected ornamental species were extracted, submitted to RT-PCR with specific primers, and amplicons obtained were sequenced. A nucleotide substitution model and phylogenetic analyses were carried out using the PAUP program. The seven sequences of CMV CP obtained showed similar identity percentages and close relationships with subgroup I isolates from other countries and hosts. CMV isolates from different regions of S?o Paulo state, Brazil (Salvia splendens, Catharanthus roseus, Nematanthus nervosus (=Hypocyrta nervosa), Impatiens walleriana, Eucharis grandiflora and Commelina sp.) formed a monophyletic group, indicating a possible common origin. It was found that when lily sequences of CMV only from different geographic regions were compared, Brazilian isolates shared the same common ancestor with those from Poland and Taiwan. Furthermore, this monophyletic group presented a quite basal position.
