Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli

Background: Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America. It does not cause human disease, but it can be mistaken for the etiologic agent of Chagas disease, Trypanosoma cruzi. We have sequenced the T. rangeli genome to provide new tools for elucidating the distinct and intriguing biology of this species and the key pathways related to interaction with its arthropod and mammalian hosts.  Methodology/Principal Findings: The T. rangeli haploid genome is ,24 Mb in length, and is the smallest and least repetitive trypanosomatid genome sequenced thus far. This parasite genome has shorter subtelomeric sequences compared to those of T. cruzi and T. brucei; displays intraspecific karyotype variability and lacks minichromosomes. Of the predicted 7,613 protein coding sequences, functional annotations could be determined for 2,415, while 5,043 are hypothetical proteins, some with evidence of protein expression. 7,101 genes (93%) are shared with other trypanosomatids that infect humans. An ortholog of the dcl2 gene involved in the T. brucei RNAi pathway was found in T. rangeli, but the RNAi machinery is non-functional since the other genes in this pathway are pseudogenized. T. rangeli is highly susceptible to oxidative stress, a phenotype that may be explained by a smaller number of anti-oxidant defense enzymes and heatshock proteins.  Conclusions/Significance: Phylogenetic comparison of nuclear and mitochondrial genes indicates that T. rangeli and T. cruzi are equidistant from T. brucei. In addition to revealing new aspects of trypanosome co-evolution within the vertebrate and invertebrate hosts, comparative genomic analysis with pathogenic trypanosomatids provides valuable new information that can be further explored with the aim of developing better diagnostic tools and/or therapeutic targets

DNA Barcoding Bromeliaceae: Achievements and Pitfalls

<div><h3>Background</h3><p>DNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL) recommended the two-marker combination <em>rbcL</em>/<em>matK</em> as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost.</p> <h3>Methodology/Principal Findings</h3><p>It is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding <em>markers</em> for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, <em>trnH–psbA</em>, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank's <em>matK</em> data set. Bromeliaceae's sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%). Species paraphyly was a common feature in our sampling.</p> <h3>Conclusions/Significance</h3><p>Our results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to discriminate species in these complex botanical groups.</p> </div

Efeito do extrato aquoso de Sida cordifolia na regeneração hepática após hepatectomia parcial

Introdução: O uso de plantas medicinais para o tratamento de patologias humanas tem aumentado em todo mundo. Muitas delas são usadas por administração oral, e após a absorção podem afetar muitos órgãos. Objetivo: Esse estudo, tem como objetivo verificar o efeito do extrato aquoso de Sida cordifolia, popularmente conhecida no Brasil como “malva-branca”, na regeneração hepática. Métodos: Vinte ratos foram divididos em 4 grupos: controle, Sida 100, Sida 200 e Sida 400. Os animais foram submetidos a administração oral de água destilada, 100, 200 e 400 mg/kg de extrato aquoso de Sida cordifolia, respectivamente. Imediatamente após, foi realizada hepatectomia parcial 67%. Vinte quatro horas após, os fígados foram removidos. A regeneração hepática foi avaliada por imunohistoquímica (PCNA), usando o anticorpo monoclonal PC-10. Resultados: Os grupos Sida100 e Sida200 mostraram índices de regeneração hepática maiores que o grupo controle (p<0.001 e p<0.05, respectivamente). Conclusão: O extrato aquoso de Sida cordifolia estimula a regeneração hepática após hepatectomia parcial a 67% em ratos. _________________________________________________________________________________________ ABSTRACT: Purpose: The use of medicinal plants for the treatment of human diseases has increased worldwide. Many of them are used by oral administration and, after absorption, may affect many organs. Therefore, this study aimed at assessing the effects of the aqueous extract of Sida cordifolia leaves, popularly known in Brazil as “malva-branca”, on liver regeneration. Methods: Twenty rats were divided into four groups: control, Sida100, Sida200 and Sida400 groups. All animals were submitted to oral administration of distilled water, 100, 200 and 400 mg/kg of the aqueous extract of Sida cordifolia, respectively. Immediately after this, they underwent 67% partial hepatectomy. Twenty four hours later, their livers were removed. Hepatic regeneration was assessed by immunohistochemical staining for proliferating cell nuclear antigen (PCNA) using the PC-10 monoclonal antibody. Results: Sida100 and Sida200 groups disclosed higher liver regeneration indices than control group (p<0.001 and p<0.05, respectively). Conclusion: The aqueous extract of Sida cordifolia stimulates liver regeneration after 67% partial hepatectomy in rats

Microbiological quality in the flour and starch cassava processing in traditional and model unit

O objetivo deste trabalho foi avaliar a qualidade microbiológica de farinha e fécula durante as diferentes etapas do processamento de mandioca, em unidades tradicionais e em uma unidade modelo. Foram determinados índices de coliformes totais e termotolerantes, Bacillus cereus, Salmonela spp., bactérias e fungos nas farinhas e féculas. Não foram observadas presenças de B. cereus e Salmonella spp. na farinha e fécula de mandioca produzidas nas unidades estudadas. A incidência microbiana diminui com o avanço da etapa do processamento para obtenção de farinha e foi menor na unidade modelo. Após o processo de torra, a carga microbiana estava de acordo com os valores preconizados pela legislação brasileira, concluindo-se que essa etapa pode ser considerada como crítica na obtenção de farinha. Na obtenção de fécula, a carga microbiana nas unidades tradicionais são maiores que na modelo, e o aumento do número de extrações promove o aumento da incidência de microrganismos, sendo recomendadas apenas quatro extrações. ______________________________________________________________________________________ ABSTRACT: The objective of this research was to evaluate microbiological contamination in the flour and starch during cassava processing in traditional and model units. The total and fecal coliforms indexes, Bacillus cereus, Salmonella, bacteria, yeast and fungi were determined. Bacillus cereus and Salmonella were not detected in any sample. The incidence of microorganisms decreased along the processing to obtain cassava flour, and is lower in model unit. After the roasting process, the microbial load was below the values established by the Brazilian legislation, and can be regarded as a critical step in obtaining cassava flour. Concerning starch production, the microbial load in the traditional units was higher than in the model units, and the increase of the extraction steps has promoted the growth of microorganisms. It’s recommended the used of only 4 extractions

Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains

Ruiz JC, D'Afonseca V, Silva A, et al. Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains. PLoS ONE. 2011;6(4): e18551.Background: Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity. Methodology and Findings: We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in genomic architecture, gene content and genetic order. When C. pseudotuberculosis was compared with other Corynebacterium species, it became evident that this pathogenic species has lost numerous genes, resulting in one of the smallest genomes in the genus. Other differences that could be part of the adaptation to pathogenicity include a lower GC content, of about 52%, and a reduced gene repertoire. The C. pseudotuberculosis genome also includes seven putative pathogenicity islands, which contain several classical virulence factors, including genes for fimbrial subunits, adhesion factors, iron uptake and secreted toxins. Additionally, all of the virulence factors in the islands have characteristics that indicate horizontal transfer. Conclusions: These particular genome characteristics of C. pseudotuberculosis, as well as its acquired virulence factors in pathogenicity islands, provide evidence of its lifestyle and of the pathogenicity pathways used by this pathogen in the infection process. All genomes cited in this study are available in the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank/) under accession numbers CP001809 and CP001829

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016