Saint Petersburg Academic University

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.

SUMMARY: Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website. AVAILABILITY: http://bioinf.spbau.ru/quast . SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis. An integrated transcriptome, genome, methylome and proteome analysis of over 200 lung adenocarcinomas reveals high rates of somatic mutations, 18 statistically significantly mutated genes including RIT1 and MGA, splicing changes, and alterations in MAPK and PI(3)K pathway activity. This report from The Cancer Genome Atlas Research Network presents molecular profiling of 230 resected untreated lung adenocarcinomas. Integrated analyses of transcriptome, genome, methylome and proteome collectively identify high rates of somatic mutation, significantly mutated genes including RIT1 and MGA, splicing alterations driven by somatic genomic changes, and point to as yet unidentified lesions that alter MAPK and PI(3)K pathway activity. These data establish a foundation for classification and further investigations of the leading cause of cancer death worldwide.

Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas. Our analyses identified three molecular subclasses of oesophageal squamous cell carcinomas, but none showed evidence for an aetiological role of human papillomavirus. Squamous cell carcinomas showed frequent genomic amplifications of CCND1 and SOX2 and/or TP63, whereas ERBB2, VEGFA and GATA4 and GATA6 were more commonly amplified in adenocarcinomas. Oesophageal adenocarcinomas strongly resembled the chromosomally unstable variant of gastric adenocarcinoma, suggesting that these cancers could be considered a single disease entity. However, some molecular features, including DNA hypermethylation, occurred disproportionally in oesophageal adenocarcinomas. These data provide a framework to facilitate more rational categorization of these tumours and a foundation for new therapies. The Cancer Genome Atlas Research Network report integrated genomic and molecular analyses of 164 squamous cell carcinomas and adenocarcinomas of the oesophagus; they find genomic and molecular features that differentiate squamous and adenocarcinomas of the oesophagus, and strong similarities between oesophageal adenocarcinomas and the chromosomally unstable variant of gastric adenocarcinoma, suggesting that gastroesophageal adenocarcinoma is a single disease entity. The Cancer Genome Atlas Research Network reports integrated genomic and molecular analyses of 164 squamous cell carcinomas and adenocarcinomas of the oesophagus. They identify genomic and molecular features that differentiate oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. They find that the genomic profiles of oesophageal adenocarcinomas are more similar to those for gastric adenocarcinoma, suggesting that these might be classified together. Separate consideration of adenocarcinoma and squamous cell carcinoma—and further molecular characterization of these cancers—may be helpful in clinical trials and for developing targeted drug therapies.

Recent advances in single-cell genomics provide an alternative to largely gene-centric metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria. However, single-cell assembly projects are challenging due to (i) the highly nonuniform read coverage and (ii) a greatly elevated number of chimeric reads and read pairs. While recently developed single-cell assemblers have addressed the former challenge, methods for assembling highly chimeric reads remain poorly explored. We present algorithms for identifying chimeric edges and resolving complex bulges in de Bruijn graphs, which significantly improve single-cell assemblies. We further describe applications of the single-cell assembler SPAdes to a new approach for capturing and sequencing "microbial dark matter" that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes from the mini-metagenome at once. On single-cell bacterial datasets, SPAdes improves on the recently developed E+V-SC and IDBA-UD assemblers specifically designed for single-cell sequencing. For standard (cultivated monostrain) datasets, SPAdes also improves on A5, ABySS, CLC, EULER-SR, Ray, SOAPdenovo, and Velvet. Thus, recently developed single-cell assemblers not only enable single-cell sequencing, but also improve on conventional assemblers on their own turf. SPAdes is available for free online download under a GPLv2 license.

Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data usually come up short in single-cell sequencing projects, algorithms actually used for single-cell error correction have been so far very simplistic.We introduce several novel algorithms based on Hamming graphs and Bayesian subclustering in our new error correction tool BAYESHAMMER. While BAYESHAMMER was designed for single-cell sequencing, we demonstrate that it also improves on existing error correction tools for multi-cell sequencing data while working much faster on real-life datasets. We benchmark BAYESHAMMER on both k-mer counts and actual assembly results with the SPADES genome assembler.

We propose metamaterials for THz frequencies based on multilayer graphene structures. We calculate the dielectric permittivity tensor of the effective nonlocal medium with a periodic stack of graphene layers and demonstrate that tuning from elliptic to hyperbolic dispersion can be achieved with an external gate voltage. We reveal that such graphene structures can demonstrate a giant Purcell effect that can be used for boosting the THz emission in semiconductor devices. Tunability of these structures can be enhanced further with an external magnetic field which leads to the unconventional hybridization of the TE and TM polarized waves.

Theoretical model for the growth of semiconductor nanowires is developed, which enables one to determine the growth conditions under which the formation of nanowires is possible. General expression for the nanowire growth rate as function of its radius and the growth conditions is obtained and analyzed. The model also describes the transformation from cubic to hexagonal crystal phase of nanowires. It is shown that the observed crystal structure is controlled mainly by the growth kinetics. Structural diagrams and probabilities of cubic and hexagonal phase formation are calculated as functions of supersaturation and nanowire radius within the plausible range of material parameters. Numerical estimates for the domains of phase mixing and phase purity are presented and analyzed.

Rapidly growing resistance of pathogenic bacteria to conventional antibiotics leads to inefficiency of traditional approaches of countering infections and determines the urgent need for a search of fundamentally new anti-infective drugs. Antimicrobial peptides (AMPs) of the innate immune system are promising candidates for a role of such novel antibiotics. However, some cytotoxicity of AMPs toward host cells limits their active implementation in medicine and forces attempts to design numerous structural analogs of the peptides with optimized properties. An alternative route for the successful AMPs introduction may be their usage in combination with conventional antibiotics. Synergistic antibacterial effects have been reported for a number of such combinations, however, the molecular mechanisms of the synergy remain poorly understood and little is known whether AMPs cytotoxicy for the host cells increases upon their application with antibiotics. Our study is directed to examination of a combined action of natural AMPs with different structure and mode of action (porcine protegrin 1, caprine bactenecin ChBac3.4, human alpha- and beta-defensins (HNP-1, HNP-4, hBD-2, hBD-3), human cathelicidin LL-37), and egg white lysozyme with varied antibiotic agents (gentamicin, ofloxacin, oxacillin, rifampicin, polymyxin B, silver nanoparticles) toward selected bacteria, including drug-sensitive and drug-resistant strains, as well as toward some mammalian cells (human erythrocytes, PBMC, neutrophils, murine peritoneal macrophages and Ehrlich ascites carcinoma cells). Using "checkerboard titrations" for fractional inhibitory concentration indexes evaluation, it was found that synergy in antibacterial action mainly occurs between highly membrane-active AMPs (e.g., protegrin 1, hBD-3) and antibiotics with intracellular targets (e.g., gentamicin, rifampcin), suggesting bioavailability increase as the main model of such interaction. In some combinations modulation of dynamics of AMP-bacterial membrane interaction in presence of the antibiotic was also shown. Cytotoxic effects of the same combinations toward normal eukaryotic cells were rarely synergistic. The obtained data approve that combined application of antimicrobial peptides with antibiotics or other antimicrobials is a promising strategy for further development of new approach for combating antibiotic-resistant bacteria by usage of AMP-based therapeutics. Revealing the conventional antibiotics that increase the activity of human endogenous AMPs against particular pathogens is also important for cure strategies elaboration.

From a theoretical point of view, we discuss a variety of phenomena linked to the spin and polarization degree of freedom of exciton-polaritons in semiconductor microcavities. We start with linear optical effects including the optical spin Hall effect, formation of polarization vortices and ballistic propagation of polarized exciton-polaritons. Next, the interplay between spin-dependent dynamics and Bose condensation in the 2D system of microcavity polaritons is addressed. Theoretically, this many-body system of interacting particles is described by the spinor Gross-Pitaevskii equations. These equations provide a description of the time evolution of polarized polariton fields under different conditions of optical excitation as well as an understanding of the phenomena of superfluidity, multistability and hysteresis via renormalization of the dispersion of elementary excitations. The comprehension of polarization-sensitive dynamics can be made through the introduction of several effective fields of different nature acting on the polariton pseudospin. The theory of parametric scattering of exciton-polaritons is presented, using the second quantization formalism. It is found that the combination of nonlinearity and various mechanisms of spin reorientation leads to self-organization and the formation of polarized patterns such as polarization crosses, vortices and rings. The manipulation of polariton spins can lead to various applications in signal processing, including the construction of optical logic gates and spin memory elements; the creation of spin currents; and the control of polarized signal propagation in the microcavity plane. The concept of polariton neurons is discussed in this connection.

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

Significance Biocompatible microfluidic double water-in-oil-in-water emulsion (MDE) enables in-droplet cultivation of different living species. The combination of droplet-generating machinery with FACS followed by next-generation sequencing and liquid chromatography-mass spectrometry analysis of the secretomes of encapsulated organisms yielded detailed genotype/phenotype descriptions. The MDE–FACS platform we developed enabled highly sensitive single-cell selection of predesigned activity and exploration of pairwise interactions between target and effector cells without interference from other microbiota species.

Abstract Optical bound states in the continuum (BICs) provide a way to engineer very narrow resonances in photonic crystals. The extended interaction time in these systems is particularly promising for the enhancement of nonlinear optical processes and the development of the next generation of active optical devices. However, the achievable interaction strength is limited by the purely photonic character of optical BICs. Here, we mix the optical BIC in a photonic crystal slab with excitons in the atomically thin semiconductor MoSe 2 to form nonlinear exciton-polaritons with a Rabi splitting of 27 meV, exhibiting large interaction-induced spectral blueshifts. The asymptotic BIC-like suppression of polariton radiation into the far field toward the BIC wavevector, in combination with effective reduction of the excitonic disorder through motional narrowing, results in small polariton linewidths below 3 meV. Together with a strongly wavevector-dependent Q -factor, this provides for the enhancement and control of polariton–polariton interactions and the resulting nonlinear optical effects, paving the way toward tuneable BIC-based polaritonic devices for sensing, lasing, and nonlinear optics.

We report on the Au-free molecular beam epitaxy growth of coherent GaAs nanowires directly on Si(111) substrates. The growth is catalyzed by liquid Ga droplets formed in the openings of a native oxide layer at the initial growth stage. Transmission electron microscopy studies demonstrate that the nanowires are single crystals having the zincblende structure along their length (apart from a thin wurtzite region directly below the Ga droplet), regardless of their diameter (70--80 nm) and the growth temperature range $(560--630\text{ }\ifmmode^\circ\else\textdegree\fi{}\text{C})$. We attribute the observed phase purity to a much lower surface energy of liquid Ga than that of Au-Ga alloys, which makes triple line nucleation energetically unfavorable. The change in growth catalyst to a liquid metal with a lower energy suppresses the (more usual) formation of wurtzite nuclei on surface energetic grounds. These results can provide a distinct method for the fabrication of chemically pure and stacking-fault-free zincblende nanowires of III-V compounds on silicon.

In this paper we present a facile method for the synthesis of aminated graphene derivative through simultaneous reduction and amination of graphene oxide via two-step liquid phase treatment with hydrobromic acid and ammonia solution in mild conditions. The amination degree of the obtained aminated reduced graphene oxide is of about 4 at.%, whereas C/O ratio is up to 8.8 as determined by means of X-ray photoelectron spectroscopy. The chemical reactivity of the introduced amine groups is further verified by successful test covalent bonding of the obtained aminated graphene with 3-Chlorobenzoyl chloride. The morphological features and electronic properties, namely conductivity, valence band structure and work function are studied as well, illustrating the influence of amine groups on graphene structure and physical properties. Particularly, the increase of the electrical conductivity, reduction of the work function value and tendency to form wrinkled and corrugated graphene layers are observed in the aminated graphene derivative compared to the pristine reduced graphene oxide. As obtained aminated graphene could be used for photovoltaic, biosensing and catalysis application as well as a starting material for further chemical modifications.

Cyanobacteria possess the unique capacity to naturally produce hydrocarbons from fatty acids. Hydrocarbon compositions of thirty-two strains of cyanobacteria were characterized to reveal novel structural features and insights into hydrocarbon biosynthesis in cyanobacteria. This investigation revealed new double bond (2- and 3-heptadecene) and methyl group positions (3-, 4- and 5-methylheptadecane) for a variety of strains. Additionally, results from this study and literature reports indicate that hydrocarbon production is a universal phenomenon in cyanobacteria. All cyanobacteria possess the capacity to produce hydrocarbons from fatty acids yet not all accomplish this through the same metabolic pathway. One pathway comprises a two-step conversion of fatty acids first to fatty aldehydes and then alkanes that involves a fatty acyl ACP reductase (FAAR) and aldehyde deformylating oxygenase (ADO). The second involves a polyketide synthase (PKS) pathway that first elongates the acyl chain followed by decarboxylation to produce a terminal alkene (olefin synthase, OLS). Sixty-one strains possessing the FAAR/ADO pathway and twelve strains possessing the OLS pathway were newly identified through bioinformatic analyses. Strains possessing the OLS pathway formed a cohesive phylogenetic clade with the exception of three Moorea strains and Leptolyngbya sp. PCC 6406 which may have acquired the OLS pathway via horizontal gene transfer. Hydrocarbon pathways were identified in one-hundred-forty-two strains of cyanobacteria over a broad phylogenetic range and there were no instances where both the FAAR/ADO and the OLS pathways were found together in the same genome, suggesting an unknown selective pressure maintains one or the other pathway, but not both.

We revisit the exciton mechanism of superconductivity in the framework of microcavity physics, replacing virtual excitons as a binding agent of Cooper pairs by excitations of an exciton-polariton Bose-Einstein condensate. We consider a model microcavity where a quantum well with a two-dimensional electron gas is sandwiched between two undoped quantum wells, where a polariton condensate is formed. We show that the critical temperature for superconductivity dramatically increases with the condensate population, opening a new route towards high-temperature superconductivity.

UNLABELLED: Ability to generate large RNA-Seq datasets created a demand for both de novo and reference-based transcriptome assemblers. However, while many transcriptome assemblers are now available, there is still no unified quality assessment tool for RNA-Seq assemblies. We present rnaQUAST-a tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. rnaQUAST calculates various metrics that demonstrate completeness and correctness levels of the assembled transcripts, and outputs them in a user-friendly report. AVAILABILITY AND IMPLEMENTATION: rnaQUAST is implemented in Python and is freely available at http://bioinf.spbau.ru/en/rnaquast CONTACT: ap@bioinf.spbau.ru SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We propose a novel approach for efficient tuning of optical properties of a high refractive index subwavelength nanoparticle with a magnetic Mie-type resonance by means of femtosecond laser irradiation. This concept is based on ultrafast photoinjection of dense (>10(20) cm(-3)) electron-hole plasma within such nanoparticle, drastically changing its transient dielectric permittivity. This allows manipulation by both electric and magnetic nanoparticle responses, resulting in dramatic changes of its scattering diagram and scattering cross section. We experimentally demonstrate 20% tuning of reflectance of a single silicon nanoparticle by femtosecond laser pulses with wavelength in the vicinity of the magnetic dipole resonance. Such a single-particle nanodevice enables designing of fast and ultracompact optical switchers and modulators.

A theoretical model of nanowire formation by the vapor-liquid-solid mechanism during molecular beam epitaxy and related growth techniques is presented. The model unifies the conventional adsorption-induced model, the diffusion-induced model, and the model of nucleation-mediated growth on the liquid-solid interface. The concentration of deposit atoms in the liquid alloy, the nanowire diameter, and all other characteristics of the growth process are treated dynamically as functions of the growth time. The model provides theoretical length-diameter dependences of nanowires and the dependence of the nanowire length on the technologically controlled growth conditions, such as the surface temperature and the deposition thickness. In particular, it is shown that the length-diameter curves of nanowires might convert from decreasing to increasing at a certain critical diameter and that the nanowires taper when their length becomes comparable with the adatom diffusion length on the sidewalls. The theoretical dependence of the nanowire morphology on its lateral size and length and on the surface temperature are compared to the available experimental data obtained recently for Si and nanowires.