Fast and sensitive taxonomic assignment to metagenomic contigs

MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each contig, quickly retains those that can contribute to taxonomic annotation, assigns them with robust labels and determines the contig’s taxonomic identity by weighted voting. Its fragment extraction step is suitable for the analysis of all domains of life. MMseqs2 taxonomy is 2–18× faster than state-of-the-art tools and also contains new modules for creating and manipulating taxonomic reference databases as well as reporting and visualizing taxonomic assignments

What do experimental data "say" about growth of hadronic total cross-section?

We reanalyse $\bar p p$ and $pp$ high energy data of the elastic scattering above $\sqrt{s}=5$ GeV on the total cross-section $\sigma_{tot}$ and on the forward $\rho$-ratio for various models of Pomeron, utilizing two methods. The first one is based on analytic amplitudes, the other one relies on assumptions for $\sigma_{tot}$ and on dispersion relation for $\rho$. We argue that it is not possible, from fitting only existing data for forward scattering, to select a definite asymptotic growth with the energy of $\sigma_{tot}$. We find equivalent fits to the data together with a logarithmic Pomeron giving a behavior $\sigma_{tot} \propto \ln ^\gamma s$, $\gamma\in [0.5,2.20]$ and with a supercritical Pomeron giving a behavior $\sigma_{tot} \propto s^\epsilon$, $\epsilon\in [0.01,0.10]$.Comment: LaTeX, 18 pages, 5 eps figures included, to be published in Il Nuovo Ciment

Vortex lattices in a stirred Bose-Einstein condensate

We stir with a focused laser beam a Bose-Einstein condensate of $^{87}$Rb atoms confined in a magnetic trap. We observe the formation of a single vortex for a stirring frequency exceeding a critical value. At larger rotation frequencies we produce states of the condensate for which up to eleven vortices are simultaneously present. We present measurements of the decay of a vortex array once the stirring laser beam is removed

Tejaas: reverse regression increases power for detecting trans-eQTLs

Trans-acting expression quantitative trait loci (trans-eQTLs) account for ≥70% expression heritability and could therefore facilitate uncovering mechanisms underlying the origination of complex diseases. Identifying trans-eQTLs is challenging because of small effect sizes, tissue specificity, and a severe multiple-testing burden. Tejaas predicts trans-eQTLs by performing L2-regularized “reverse” multiple regression of each SNP on all genes, aggregating evidence from many small trans-effects while being unaffected by the strong expression correlations. Combined with a novel unsupervised k-nearest neighbor method to remove confounders, Tejaas predicts 18851 unique trans-eQTLs across 49 tissues from GTEx. They are enriched in open chromatin, enhancers, and other regulatory regions. Many overlap with disease-associated SNPs, pointing to tissue-specific transcriptional regulation mechanisms.Fil: Banerjee, Saikat. Max Planck Institute For Biophysical Chemistry; AlemaniaFil: Simonetti, Franco Lucio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Max Planck Institute For Biophysical Chemistry; AlemaniaFil: Detrois, Kira E.. Max Planck Institute For Biophysical Chemistry; Alemania. Universität Göttingen; AlemaniaFil: Kaphle, Anubhav. Universität Göttingen; Alemania. Max Planck Institute For Biophysical Chemistry; AlemaniaFil: Mitra, Raktim. Indian Institute of Technology; IndiaFil: Nagial, Rahul. Indian Institute of Technology; IndiaFil: Söding, Johannes. Max Planck Institute For Biophysical Chemistry; Alemania. University of Göttingen; Alemani

A Conserved GA Element in TATA-Less RNA Polymerase II Promoters

Initiation of RNA polymerase (Pol) II transcription requires assembly of the pre-initiation complex (PIC) at the promoter. In the classical view, PIC assembly starts with binding of the TATA box-binding protein (TBP) to the TATA box. However, a TATA box occurs in only 15% of promoters in the yeast Saccharomyces cerevisiae, posing the question how most yeast promoters nucleate PIC assembly. Here we show that one third of all yeast promoters contain a novel conserved DNA element, the GA element (GAE), that generally does not co-occur with the TATA box. The distance of the GAE to the transcription start site (TSS) resembles the distance of the TATA box to the TSS. The TATA-less TMT1 core promoter contains a GAE, recruits TBP, and supports formation of a TBP-TFIIB-DNA-complex. Mutation of the promoter region surrounding the GAE abolishes transcription in vivo and in vitro. A 32-nucleotide promoter region containing the GAE can functionally substitute for the TATA box in a TATA-containing promoter. This identifies the GAE as a conserved promoter element in TATA-less promoters

Weakly bound atomic trimers in ultracold traps

The experimental three-atom recombination coefficients of the atomic states $^{23}$Na$|F=1,m_F=-1>$, $^{87}$Rb$|F=1,m_F=-1>$ and $^{85}$Rb$|F=2,m_F=-2>$, together with the corresponding two-body scattering lengths, allow predictions of the trimer bound state energies for such systems in a trap. The recombination parameter is given as a function of the weakly bound trimer energies, which are in the interval $1<m(a/\hbar)^2 E_3< 6.9$ for large positive scattering lengths, $a$. The contribution of a deep-bound state to our prediction, in the case of $^{85}$Rb$|F=2,m_F=-2>$, for a particular trap, is shown to be relatively small.Comment: 5 pages, 1 figur

Excitation-assisted inelastic processes in trapped Bose-Einstein condensates

We find that inelastic collisional processes in Bose-Einstein condensates induce local variations of the mean-field interparticle interaction and are accompanied by the creation/annihilation of elementary excitation. The physical picture is demonstrated for the case of three body recombination in a trapped condensate. For a high trap barrier the production of high energy trapped single particle excitations results in a strong increase of the loss rate of atoms from the condensate.Comment: 4 pages, no figure

Lysine/RNA-interactions drive and regulate biomolecular condensation.

Cells form and use biomolecular condensates to execute biochemical reactions. The molecular properties of non-membrane-bound condensates are directly connected to the amino acid content of disordered protein regions. Lysine plays an important role in cellular function, but little is known about its role in biomolecular condensation. Here we show that protein disorder is abundant in protein/RNA granules and lysine is enriched in disordered regions of proteins in P-bodies compared to the entire human disordered proteome. Lysine-rich polypeptides phase separate into lysine/RNA-coacervates that are more dynamic and differ at the molecular level from arginine/RNA-coacervates. Consistent with the ability of lysine to drive phase separation, lysine-rich variants of the Alzheimer's disease-linked protein tau undergo coacervation with RNA in vitro and bind to stress granules in cells. Acetylation of lysine reverses liquid-liquid phase separation and reduces colocalization of tau with stress granules. Our study establishes lysine as an important regulator of cellular condensation

Phase-fluctuating 3D condensates in elongated traps

We find that in very elongated 3D trapped Bose gases, even at temperatures far below the BEC transition temperature Tc, the equilibrium state will be a 3D condensate with fluctuating phase (quasicondensate). At sufficiently low temperatures the phase fluctuations are suppressed and the quasicondensate turns into a true condensate. The presence of the phase fluctuations allows for extending thermometry of Bose-condensed gases well below those established in current experiments.Comment: 5 pages REVTeX, 3 figures, misprints correcte