The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Data Mining - Concepts and Techniques.

Microbial decolouration of azo dyes: a review.

Neotropical Rainforest Mammals. A Field Guide, Louise H. Emmons. University of Chicago Press, Chicago (1990), xiv, Illustrations by François Feer, +281. Price $45·00 hardback, $19·95 paperback

Almost all known human specific parasites have been found in ancient feces. A review of the paleoparasitological helminth and intestinal protozoa findings available in the literature is presented. We also report the new paleoparasitologic findings from the examination performed in samples collected in New and Old World archaeological sites. New finds of ancylostomid, Ascaris lumbricoides, Trichuris trichiura, Enterobius vermicularis, Trichostrongylus spp., Diphyllobothrium latum, Hymenolepis nana and Acantocephalan eggs are reported. According to the findings, it is probable that A. lumbricoides was originally a human parasite. Human ancylostomids, A. lumbricoides and T. trichiura, found in the New World in pre-Columbian times, have not been introduced into the Americas by land via Beringia. These parasites could not supported the cold climate of the region. Nomadic prehistoric humans that have crossed the Bering Land Bridge from Asia to the Americas in the last glaciation, probably during generations, would have lost these parasites, which life cycles need warm temperatures in the soil to be transmitted from host to host. Alternative routes are discussed for human parasite introduction into the Americas.

https://www.arca.fiocruz.br/bitstream/icict/24719/2/HumanIntestinal.pdf

Human intestinal parasites in the past: new findings and a review

The study of feces of terrestrial mammals brings out biological and ecological data such as the species presence, diet, behaviour, territory, parasitic fauna, and home-range use, which can be applied for conservation projects and support paleoecological research that use coprolites as the main source of study. Although the new biotechnological techniques allow more accurate data, the diagnosis based on morphometric analyses permits the primary identification of the taxonomic group origin to support the best choice of subsequent analyses. We present the compilation list of fecal shape and measurements available in the literature published in North America, Eastern and Southern Africa, Europe, and new data from Brazil. Shape and diameters are the best characteristics for taxonomic identification. Feces were assembled in 9 groups that reflect the Order, sometimes the Family, and even their common origin.

/pdf/terrestrial-mammal-feces-a-morphometric-summary-and-4xgcb54aqd.pdf

Terrestrial mammal feces: a morphometric summary and description

The authors present a review of records of intestinal parasitic helminths from animals in human archaeological remains, reported since the emergence of paleopathological studies. The objective was to relate paleoparasitological findings to geographic, biotic, and abiotic factors from the environment in which the prehistoric populations lived, and understand some aspects related to the process of human dispersion and biological and cultural evolution. Modification of eating habits and the incorporation of new cultural practices are analyzed from the perspective of zoonoses from prehistory to the present day, especially in Brazilian indigenous populations. Three tables identifying the helminths, their natural hosts, dates, and sites of archaeological findings complete this review. In conclusion, various zoonoses known today have occurred since antiquity, and these data, combined with studies on the emergence and reemergence of diseases, could make possible to compose scenarios for the future.

/pdf/animal-helminths-in-human-archaeological-remains-a-review-of-2mjomwrlnb.pdf

Animal helminths in human archaeological remains: a review of zoonoses in the past

The identification of parasites from ancient cultures expands our list of parasites infective to extant humans. A partially mummified human body from the archeological site of Lapa do Boquete, Minas Gerais State, Brazil, was recently discovered. It was interred between 600 and 1,200 yr ago. Dietary analysis showed that the mummified body was from a society that had a mixed subsistence of agriculture and gathering of wild foods. Coprolites from the body contained numerous helminth eggs. The eggs were identified as those of Echinostoma sp. and hookworm. Hookworm infection in pre-Columbian populations is already established, but this is the first evidence of Echinostoma sp. eggs found in human coprolites. The diagnosis of a true infection, as opposed to false parasitism, is discussed. The possibility of Echinostoma ilocanum infection is discussed, as this is a common species found in humans in the Asiatic region, which could have been introduced in South America in the pre-Columbian period. Alternative possibilities are also considered, including indigenous Brazilian Echinostoma species.

/pdf/the-finding-of-echinostoma-trematoda-digenea-and-hookworm-3z7egs03ya.pdf

The Finding of Echinostoma (Trematoda: Digenea) and Hookworm Eggs in Coprolites Collected From a Brazilian Mummified Body Dated 600–1,200 Years Before Present

The occurrence of certain parasites in human groups from different regions has been used to study the geographical origin of both hosts and parasites. The presence of hookworm infection in an isolated tribe in remote regions of Paraguay led to speculations about its origin, since the prehistoric migrations through the Behring Land Bridge could not have brought the parasite, which needs for its mantenance a temperature of about 22oC in the soil. It was then proposed that only transpacific migrations of Asiatic populations could have brought the parasite to America. This discussion dates back to the beginning of this Century and it was only with recent paleoparasitological findings that it arose again. This paper is a review of hookworm findings in archaeological material and suggests possible routes followed by their hosts to reach the New World.

Hookworms and the peopling of America

Zika virus (ZIKV) was first isolated in 1947 in primates in Uganda, West Africa. The virus remained confined to the equatorial regions of Africa and Asia, cycling between infecting monkeys, arboreal mosquitoes, and occasionally humans. The ZIKV Asiatic strain was probably introduced into Brazil in or around late 2013. Presently, ZIKV is in contact with the rich biodiversity in all Brazilian biomes, bordering on other Latin American countries. Infections in Brazilian primates have been reported recently, but the overall impact of this virus on wildlife in the Americas is still unknown. The current epidemic in the Americas requires knowledge on the role of mammals, especially nonhuman primates (NHPs), in ZIKV transmission to humans. The article discusses the available data on ZIKV in host animals and issues of biodiversity, rapid environmental change, and impact on human health in megadiverse Latin American countries. The authors reviewed scientific articles and recent news stories on ZIKV in animals, showing that 47 animal species from three orders (mammals, reptiles, and birds) have been investigated for the potential to establish a sylvatic cycle. The review aims to contribute to epidemiological studies and the knowledge on the natural history of ZIKV. The article concludes with questions that require urgent attention in epidemiological studies involving wildlife in order to understand their role as ZIKV hosts and to effectively control the epidemic.

/pdf/animals-in-the-zika-virus-life-cycle-what-to-expect-from-4qcuokcrtw.pdf

Marcia Chame

Papers

Terrestrial mammal feces: a morphometric summary and description

Animal helminths in human archaeological remains: a review of zoonoses in the past

The Finding of Echinostoma (Trematoda: Digenea) and Hookworm Eggs in Coprolites Collected From a Brazilian Mummified Body Dated 600–1,200 Years Before Present

Hookworms and the peopling of America

Animals in the Zika virus life cycle: what to expect from megadiverse Latin American countries