Analysis of Chromobacterium sp. natural isolates from different Brazilian ecosystems

<p>Abstract</p> <p>Background</p> <p><it>Chromobacterium violaceum </it>is a free-living bacterium able to survive under diverse environmental conditions. In this study we evaluate the genetic and physiological diversity of <it>Chromobacterium </it>sp. isolates from three Brazilian ecosystems: Brazilian Savannah (Cerrado), Atlantic Rain Forest and Amazon Rain Forest. We have analyzed the diversity with molecular approaches (16S rRNA gene sequences and amplified ribosomal DNA restriction analysis) and phenotypic surveys of antibiotic resistance and biochemistry profiles.</p> <p>Results</p> <p>In general, the clusters based on physiological profiles included isolates from two or more geographical locations indicating that they are not restricted to a single ecosystem. The isolates from Brazilian Savannah presented greater physiologic diversity and their biochemical profile was the most variable of all groupings. The isolates recovered from Amazon and Atlantic Rain Forests presented the most similar biochemical characteristics to the <it>Chromobacterium violaceum </it>ATCC 12472 strain. Clusters based on biochemical profiles were congruent with clusters obtained by the 16S rRNA gene tree. According to the phylogenetic analyses, isolates from the Amazon Rain Forest and Savannah displayed a closer relationship to the <it>Chromobacterium violaceum </it>ATCC 12472. Furthermore, 16S rRNA gene tree revealed a good correlation between phylogenetic clustering and geographic origin.</p> <p>Conclusion</p> <p>The physiological analyses clearly demonstrate the high biochemical versatility found in the <it>C. violaceum </it>genome and molecular methods allowed to detect the intra and inter-population diversity of isolates from three Brazilian ecosystems.</p

The Genetic History of Indigenous Populations of the Peruvian and Bolivian Altiplano: The Legacy of the Uros

The Altiplano region of the South American Andes is marked by an inhospitable climate to which the autochthonous human populations adapted and then developed great ancient civilizations, such as the Tiwanaku culture and the Inca Empire. Since pre-Columbian times, different rulers established themselves around the Titicaca and Poopo Lakes. By the time of the arrival of Spaniards, Aymara and Quechua languages were predominant on the Altiplano under the rule of the Incas, although the occurrence of other spoken languages, such as Puquina and Uruquilla, suggests the existence of different ethnic groups in this region. In this study, we focused on the pre-Columbian history of the autochthonous Altiplano populations, particularly the Uros ethnic group, which claims to directly descend from the first settlers of the Andes, and some linguists suggest they might otherwise be related to Arawak speaking groups from the Amazon. Using phylogeographic, population structure and spatial genetic analyses of Y-chromosome and mtDNA data, we inferred the genetic relationships among Uros populations (Los Uros from Peru, Uru-Chipaya and Uru-Poopo from Bolivia), and compared their haplotype profiles with eight Aymara, nine Quechua and two Arawak (Machiguenga and Yanesha) speaking populations from Peru and Bolivia. Our results indicated that Uros populations stand out among the Altiplano populations, while appearing more closely related to the Aymara and Quechua from Lake Titicaca and surrounding regions than to the Amazon Arawaks. Moreover, the Uros populations from Peru and Bolivia are genetically differentiated from each other, indicating a high heterogeneity in this ethnic group. Finally, our results support the distinctive ancestry for the Uros populations of Peru and Bolivia, which are likely derived from ancient Andean lineages that were partially replaced during more recent farming expansion events and the establishment of complex civilizations in the Andes

Molecular systematics of the genus Artibeus (Chiroptera

a b s t r a c t A molecular phylogeny of the genus Artibeus using 19 of the 20 recognized species, many with samples from a broad geographic range, is presented. The analysis shows a clear distinction between the two subgenera (or genera), the &apos;large&apos; Artibeus and the &apos;small&apos; Dermanura, in both mitochondrial and nuclear genes. The placement and status of A. concolor remains inconclusive and is presented as the third subgenus Koopmania. The phylogenies and divergence time estimates show a marked influence of the Andes in the formation of the subgenera and the main lineages inside each subgenus. Nuclear genes showed a highly incomplete lineage sorting among species inside subgenera Artibeus and Dermanura. Indeed, shared alleles were also found between Artibeus and Koopmania, which are presumed to have split apart during the Miocene, showing that great care should be taken in using these markers. Cytochrome-b gene divergences and monophyly analyses suggest that A. lituratus and A. intermedius are indeed conspecifics. These analyses also suggested the existence of at least four &apos;new&apos; species revealing a significant cryptic diversity inside the genus

From cheek swabs to consensus sequences : an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes

Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users. Results: Here we present an ‘A to Z’ protocol for obtaining complete human mitochondrial (mtDNA) genomes – from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). Conclusions: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual ‘modules’ can be swapped out to suit available resources

Time-Course of Changes in Physiological, Psychological and Performance markers Following a Functional-Fitness Competition

International Journal of Exercise Science 12(3): 904-918, 2019. Functional Fitness Training (FFT) programs are characterized by utilizing a high volume of training and using a variety of high intensity exercises. While FFT are growing in the number of practitioners and popularity, the relationship between physiological biomarkers and subjective scales in the specific context of FFT has not yet been evaluated in the literature. The purpose of the present study was to monitor the time-course response of cytokines (IL-10 and 1L-1b), immune variables (C-reactive protein -CRP and immunoglobulin A-IgA), hormonal milieu (cortisol-C, total testosterone-TT, free testosterone-FT and testosterone/cortisol-T/C ratio), creatine kinase-CK, muscle performance (countermovement jump height) and perceived well-being (WB) following a functional fitness competition. Nine amateur male athletes (age 27.1 ± 4.1 years; training experience 2.2 ± 1.3 years) completed five workouts over three consecutive days of FFT-competition. All variables were measured before, 24 h, 48 h, and 72 h following the last day of competition. The FFT-competition induced a decrease in IL10/IL1bratio approximately 5% after 24h, 21% after 48h and 31% after 72h. Delta T/C ratio remained unchanged during the post-competition period. IgA displayed a significant increase 24h and 72h post FFT-competition. The WB status score was higher 72h after the FFT-competition as compared with pre-competition. The present findings suggest that FFT-competition induces transient changes in some inflammatory and hormonal biomarkers, and perceived well-being seems to be efficient to detect changes in muscle performance