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)

Soil Nutrient Bioavailability—A Mechanistic Approach

Morphometric tools for landmark data: geometry and biology

Rodents are the most abundant and diversified order of living mammals in the world. Already since the Middle Ages we know that they can contribute to human disease, as black rats were associated with distribution of plague. However, also in modern times rodents form a threat for public health. In this review article a large number of pathogens that are directly or indirectly transmitted by rodents are described. Moreover, a simplified rodent disease model is discussed.

Rodent-borne diseases and their risks for public health

BACKGROUND The extent of urban areas is increasing around the world, and most humans now live in cities. Urbanization results in dramatic environmental change, including increased temperatures, more impervious surface cover, altered hydrology, and elevated pollution. Urban areas also host more non-native species and reduced abundance and diversity of many native species. These environmental changes brought by global urbanization are creating novel ecosystems with unknown consequences for the evolution of life. Here, we consider how early human settlements led to the evolution of human commensals, including some of the most notorious pests and disease vectors. We also comprehensively review how contemporary urbanization affects the evolution of species that coinhabit cities. ADVANCES A recent surge of research shows that urbanization affects both nonadaptive and adaptive evolution. Some of the clearest results of urban evolution show that cities elevate the strength of random genetic drift (stochastic changes in allele frequencies) and restrict gene flow (the movement of alleles between populations due to dispersal and mating). Populations of native species in cities often represent either relicts that predate urbanization or populations that established after a city formed. Both scenarios frequently result in a loss of genetic diversity within populations and increased differentiation between populations. Fragmentation and urban infrastructure also create barriers to dispersal, and consequently, gene flow is often reduced among city populations, which further contributes to genetic differentiation between populations. The influence of urbanization on mutation and adaptive evolution are less clear. A small number of studies suggest that industrial pollution can elevate mutation rates, but the pervasiveness of this effect is unknown. A better studied phenomenon are the effects of urbanization on evolution by natural selection. A growing number of studies show that plant and animal populations experience divergent selection between urban and nonurban environments. This divergent selection has led to adaptive evolution in life history, morphology, physiology, behavior, and reproductive traits. These adaptations typically evolve in response to pesticide use, pollution, local climate, or the physical structure of cities. Despite these important results, the genetic basis of adaptive evolution is known from only a few cases. Most studies also examine only a few populations in one city, and experimental validation is rare. OUTLOOK The study of evolution in urban areas provides insights into both fundamental and applied problems in biology. The thousands of cities throughout the world share some features while differing in other aspects related to their age, historical context, governmental policies, and local climate. Thus, the phenomenon of global urbanization represents an unintended but highly replicated global study of experimental evolution. We can harness this global urban experiment to understand the repeatability and pace of evolution in response to human activity. Among the most important unresolved questions is, how often do native and exotic species adapt to the particular environmental challenges found in cities? Such adaptations could be the difference as to whether a species persists or vanishes from urban areas. In this way, the study of urban evolution can help us understand how evolution in populations may contribute to conservation of rare species, and how populations can be managed to facilitate the establishment of resilient and sustainable urban ecosystems. In a similar way, understanding evolution in urban areas can lead to improved human health. For example, human pests frequently adapt to pesticides and evade control efforts because of our limited understanding of the size of populations and movement of individuals. Applied evolutionary studies could lead to more effective mitigation of pests and disease agents. The study of urban evolution has rapidly become an important frontier in biology, with implications for healthy and sustainable human populations in urban ecosystems.

Evolution of life in urban environments.

Robustness of techniques for estimating rat damage and yield loss in maize fields.

The breeding pattern of the grass rat, Arvicanthis neumanni, was investigated in central Tanzania in 2002 ⁄ 2003. Nine hundred and forty-seven animals were captured in three age groups: juveniles, sub adults and adults. These age groups were present in the population for an extended duration, but there was an increase in the number of sexually active individuals and juveniles 2–3 months after the onset of the rains (December 2002–May 2003). A peak in reproductive activity occurred between January and April. Litter size ranged between 5.58 ± 0.42 and 6.1 ± 0.26 in two study sites. There were no significant differences in the number of embryos implanted in the right and left horns of the uterus of pregnant females (t22 =0 ,P > 0.05 and t36 = 1.68, P > 0.05, respectively). Sex ratio of A. neumanni was not skewed to either males or females. Breeding was seasonal and seemed to be associated with seasonal variations in primary productivity, which relates to rainfall patterns.

/pdf/breeding-patterns-of-arvicanthis-neumanni-in-central-2d1wq01lfj.pdf

Breeding patterns of Arvicanthis neumanni in central Tanzania

Molecular variability and distribution of Rice yellow mottle virus in Tanzania.

Mulungu, L.S., Belmain, S.R., Dlamini, N., Eiseb, S., Kirsten, F., Mahlaba, T., Makundi, R., Malebane, P., Von Maltitz, E., Massawe, A., Monadjem, A., Taylor, P., Tutjavi, V.

/pdf/the-ecorat-project-development-of-ecologically-based-rodent-2kxhdqf3pb.pdf

The Ecorat project: development of ecologically-based rodent management for the southern African region.

Resistance of rodents to anticoagulant rodenticides has emerged in several areas across the world. Single nucleotide mutations in the vkorc1 gene have been shown to elicit various levels of anticoagulant resistance, and these mutations are prevalent in several Rattus and Mus musculus populations. In sub-Saharan Africa, the Natal multimammate mouse, Mastomys natalensis, is one of the most damaging pests to crops, and anticoagulant poisons such as bromadiolone are frequently used to control these rodents in agricultural fields. Here, we investigate if vkorc1 shows any polymorphism in natural populations of M. natalensis. We sequenced the third exon of vkorc1 of 162 M. natalensis captured from 14 different agricultural sites in Morogoro Region, Tanzania. In addition to 6 SNPs in the noncoding flanking region, we detected 3 nonsynonymous SNPs in this exon: 10 animals (6.2%) carried a Leu108Val variant, 2 animals (1.2%) an Ala140Thr variant, and 1 animal (0.6 %) an Arg100His variant, all 3 in heterozygous form. Ala140Thr is just one residue from a mutation known to be involved in anticoagulant resistance in Rattus and Mus. While in vitro or in vivo experiments are needed to link vkorc1 genetic polymorphisms to level of VKOR activity and anticoagulant susceptibility, our results suggest that M. natalensis individuals may vary in their response to anticoagulant rodenticides. This is the first vkorc1 sequence data from a species outside the Rattus or Mus genera, and for the first time from a rodent species endemic to Africa.

/pdf/polymorphism-in-vkorc1-gene-of-natal-multimammate-mice-4si0dlx42f.pdf

Polymorphism in vkorc1 Gene of Natal Multimammate Mice, Mastomys natalensis, in Tanzania

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