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)

Evolution of Protein Molecules

There are two kinds of tutorial articles: those that provide a primer on an established topic and those that let us in on the ground floor of something of emerging importance. The first type of tutorial can have a noted expert who has been gracious (and brave) enough to write a field guide about a particular topic. The other sort of tutorial typically involves researchers who have each been laboring on a topic for some years. Both sorts of tutorial articles are very much desired. But we, as an editorial board for both Systems and Transactions, know that there has been no logical place for them in the AESS until this series was started several years ago. With these tutorials, we hope to continue to give them a home, a welcome, and provide a service to our membership. We do not intend to publish tutorials on a regular basis, but we hope to deliver them once or twice per year. We need and welcome good, useful tutorial articles (both kinds) in relevant AESS areas. If you, the reader, can offer a topic of interest and an author to write about it, please contact us. Self-nominations are welcome, and even more ideal is a suggestion of an article that the editor(s) can solicit. All articles will be reviewed in detail. Criteria on which they will be judged include their clarity of presentation, relevance, and likely audience, and, of course, their correctness and scientific merit. As to the mathematical level, the articles in this issue are a good guide: in each case the author has striven to explain complicated topics in simple-well, tutorial-terms. There should be no (or very little) novel material: the home for archival science is the Transactions Magazine, and submissions that need to be properly peer reviewed would be rerouted there. Likewise, articles that are interesting and descriptive, but lack significant tutorial content, ought more properly be submitted to the Systems Magazine.

What is a tutorial

Chemosynthetic symbioses occur in a wide range of ocean habitats, from deep-sea vents and cold seeps to whale falls and shallow-water sediments. This Review reveals the diversity and complexity of these symbioses, some of which include multiple symbiotic partners. Chemosynthetic symbioses between bacteria and marine invertebrates were discovered 30 years ago at hydrothermal vents on the Galapagos Rift. Remarkably, it took the discovery of these symbioses in the deep sea for scientists to realize that chemosynthetic symbioses occur worldwide in a wide range of habitats, including cold seeps, whale and wood falls, shallow-water coastal sediments and continental margins. The evolutionary success of these symbioses is evident from the wide range of animal groups that have established associations with chemosynthetic bacteria; at least seven animal phyla are known to host these symbionts. The diversity of the bacterial symbionts is equally high, and phylogenetic analyses have shown that these associations have evolved on multiple occasions by convergent evolution. This Review focuses on the diversity of chemosynthetic symbionts and their hosts, and examines the traits that have resulted in their evolutionary success.

Symbiotic diversity in marine animals: the art of harnessing chemosynthesis

The global geographic distribution of subseafloor sedimentary microbes and the cause(s) of that distribution are largely unexplored. Here, we show that total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. This variation is strongly correlated with mean sedimentation rate and distance from land. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9⋅1029 cells [corresponding to 4.1 petagram (Pg) C and ∼0.6% of Earth’s total living biomass]. This estimate of subseafloor sedimentary microbial abundance is roughly equal to previous estimates of total microbial abundance in seawater and total microbial abundance in soil. It is much lower than previous estimates of subseafloor sedimentary microbial abundance. In consequence, we estimate Earth’s total number of microbes and total living biomass to be, respectively, 50–78% and 10–45% lower than previous estimates.

/pdf/global-distribution-of-microbial-abundance-and-biomass-in-3tlqusko0l.pdf

Global distribution of microbial abundance and biomass in subseafloor sediment

The purpose of the present invention is to provide a nuclease that secretes natural nonpathogenic microorganisms extracellularly, has higher specific activity than conventional nucleases, and is useful in nucleolytic degradation on an industrial scale. This purpose is achieved with an extracellularly secreted nuclease derived from Streptomyces bacteria, the nuclease having specific activity equal to or greater than the specific activity of Benzonase® when supplied to double-stranded DNA for 30 minutes at 37° C. in 20 mM Tris/HCl (pH 8.5) containing 1 mM MgCl 2 and 1 mM CaCl 2 after purification, using double-stranded DNA, single-stranded DNA, and RNA as substrates.

Extracellularly secreted nuclease

Many age-dependent neurodegenerative diseases, like Alzheimer9s and Parkinson9s, are characterised by abundant inclusions of amyloid filaments. Filamentous inclusions of the proteins tau, amyloid-β (Aβ), α-synuclein and TDP-43 are the most common. Here, we used electron cryo-microscopy (cryo-EM) structure determination to show that residues 120-254 of the lysosomal type II transmembrane protein 106B (TMEM106B) also form amyloid filaments in the human brain. We solved cryo-EM structures of TMEM106B filaments from the brains of 22 individuals with neurodegenerative conditions, including sporadic and inherited tauopathies, Aβ-amyloidoses, synucleinopathies and TDP-43opathies, as well as from the brains of two neurologically normal individuals. We observed three different TMEM106B folds, with no clear relationship between folds and diseases. The presence of TMEM106B filaments correlated with that of a 29 kDa sarkosyl-insoluble fragment of the protein on Western blots. The presence of TMEM106B filaments in the brains of older, but not younger, neurologically normal individuals indicates that they form in an age-dependent manner.

https://www.biorxiv.org/content/biorxiv/early/2021/11/11/2021.11.09.467923.full.pdf

Age-Dependent Formation of TMEM106B Amyloid Filaments in Human Brain

El manejo de los Residuos SÃ³lidos Urbanos -RSU- continÃºa siendo un tema irresuelto para la gran mayorÃ­a de los paÃ­ses. El crecimiento demogrÃ¡fico, el aumento de las industrias, los cambios en patrones de consumo y las mejoras del nivel de vida son los factores que influyen directamente con la misma. Para esta parte de la regiÃ³n se observa un aumento en la tendencia de la producciÃ³n per cÃ¡pita de RSU. Asimismo, en el paÃ­s se estima que solo una pequeÃ±a porciÃ³n de los RSU generados son tratados en sitios con licencia ambiental. En efecto una informaciÃ³n sobre la gestiÃ³n integral de RSU es fundamental para iniciar con la acciÃ³n basada en el fortalecimiento de la conciencia ambiental apuntando hacia la construcciÃ³n de una sociedad 

Urban solid waste management: an environmental education strategy in Paraguay

Elemental sulfur, hydrogen sulfide, and carbon monoxide-driven dimerization of glycine at sub-millimolar concentrations: Implications for the origin of life

Masayuki Miyazaki

Papers

Extracellularly secreted nuclease

Age-Dependent Formation of TMEM106B Amyloid Filaments in Human Brain

Urban solid waste management: an environmental education strategy in Paraguay

Elemental sulfur, hydrogen sulfide, and carbon monoxide-driven dimerization of glycine at sub-millimolar concentrations: Implications for the origin of life