The complete genome sequence of the nitrile biocatalyst Rhodococcus rhodochrous ATCC BAA-870

BACKGROUND : Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst. RESULTS : The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci. CONCLUSIONS : The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.Additional file 1: SuppInfo Frederick et al. BAA-870 genome. Table S1. All sequenced Rhodococcus strains (353) according to the NCBI database (accessed 13/03/2019). Table S2. All complete sequenced Rhodococcus species ranked by release date according to the NCBI Genome database (accessed 11/03/2019). Table S3. Whole genome distance statistics between Rhodococcus rhodochrous ATCC BAA-870 and two closely matched strains. Table S4. Rhodococcus rhodochrous ATCC BAA-870 protein function breakdown based on BASys annotation COG classifications.The Department of Science and Technology (DST) Biocatalysis Initiative (Grant 0175/2013), South Africa, the CSIR Thematic Programme, the Welch Foundation (grant E-1264) and the European Science Foundation COST Action CM0701.https://bmcgenomics.biomedcentral.comam2020BiochemistryGeneticsMicrobiology and Plant Patholog

On Eigenvalues of Random Complexes

We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial-Meshulam model $X^k(n,p)$ of random $k$-dimensional simplicial complexes on $n$ vertices. We show that for $p=\Omega(\log n/n)$, the eigenvalues of these matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of $(k-2)$-dimensional faces. Garland's result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of $k$-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the higher-dimensional Laplacian spectra capture the notion of coboundary expansion - a generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every $k\geq 2$ and $n\in \mathbb{N}$, there is a $k$-dimensional complex $Y^k_n$ on $n$ vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised $k$-dimensional Laplacian lie in the interval $[1-O(1/\sqrt{n}),1+O(1/\sqrt{n})]$) but whose coboundary expansion is bounded from above by $O(\log n/n)$ and so tends to zero as $n\rightarrow \infty$; moreover, $Y^k_n$ can be taken to have vanishing integer homology in dimension less than $k$.Comment: Extended full version of an extended abstract that appeared at SoCG 2012, to appear in Israel Journal of Mathematic

New evidence of factor structure and measurement invariance of the SDQ across five European nations

The main purpose of the present study was to test the internal structure and to study the measurement invariance of the Strength and Difficulties Questionnaire (SDQ), self-reported version, in five European countries. The sample consisted of 3012 adolescents aged between 12 and 17 years (M = 14.20; SD = 0.83). The five-factor model (with correlated errors added), and the five-factor model (with correlated errors added) with the reverse-worded items allowed to cross-load on the Prosocial subscale, displayed adequate goodness of-fit indices. Multi-group confirmatory factor analysis showed that the five-factor model had partial strong measurement invariance by countries. A total of 11 of the 25 items were non-invariant across samples. The level of internal consistency of the Total difficulties scores was .84, ranging between .69 and .78 for the SDQ subscales. The findings indicate that the SDQ's scales need to be modified in various ways for screening emotional and behavioural problems in the five European countries that were analyzed

Synthesis of the cyclic heptapeptide core of callipeltin A

Macrolactonisation of a novel heptapeptide precursor with PyAOP proved to be an excellent method for preparation of the cyclic depsipeptide core of callipeltin A. The individual building blocks were obtained in high yield and selectivity and successive coupling allowed for the straightforward preparation of the linear heptapeptide from tyrosine 6 in 27% over 12 steps

Stereoselective Synthesis of a Protected Side Chain of Callipeltin A

Matteson homologations of chiral boronic esters proved to be an excellent tool for the synthesis of highly functionalized amino and hydroxy acid residues. This method provides straightforward stereoselective access to the side chain of callipeltin A, a natural marine product with interesting biological activities. Furthermore, this protocol should allow for variations in the substitution pattern in future SAR studies, simply by choosing suitable nucleophiles during the homologation steps

Granularity and scalar implicature in numerical expressions

Cummins C, Sauerland U, Solt S. Granularity and scalar implicature in numerical expressions. Linguistics and Philosophy. 2012;35(2):135-169.It has been generally assumed that certain categories of numerical expressions, such as 'more than n', 'at least n', and 'fewer than n', systematically fail to give rise to scalar implicatures in unembedded declarative contexts. Various proposals have been developed to explain this perceived absence. In this paper, we consider the relevance of scale granularity to scalar implicature, and make two novel predictions: first, that scalar implicatures are in fact available from these numerical expressions at the appropriate granularity level, and second, that these implicatures are attenuated if the numeral has been previously mentioned or is otherwise salient in the context. We present novel experimental data in support of both of these predictions, and discuss the implications of this for recent accounts of numerical quantifier usage

Под знаменем Ленина. 1966. № 214

The strategy of this paper is twofold: First, we carry out a systematic investigation of the question of what specific kind of meaning quotation marks contribute to the overall meaning of an utterance. We consider the following kinds of meaning: literal meaning (§ 2.1), conventional implicature (§ 2.2), presupposition (§ 2.3), and conversational implicature (§ 2.4). We present arguments in favor of a pragmatic analysis of quotation marks, claiming that the notion of conversational implicature seems to be the most promising alternative: All general features of this kind of meaning are met by quotational constructions. Nonetheless, an approach based on conversational implicatures faces some problems when taking direct and pure quotations into account, namely effects on truth-conditions and, allegedly, on grammaticality. Thus, our second aim is to propose acceptable solutions to these criticisms in § 3. Finally, in § 4, we consider how a radical pragmatic account of quotation could be integrated into a Neo-Gricean architecture of the semantics/pragmatics-interface

The complete genome sequence of the nitrile biocatalyst Rhodocccus rhodochrous ATCC BAA-870

BACKGROUND: Rhodococci are industrially important soil-dwelling Gram-positive bacteria that are well known for both nitrile hydrolysis and oxidative metabolism of aromatics. Rhodococcus rhodochrous ATCC BAA-870 is capable of metabolising a wide range of aliphatic and aromatic nitriles and amides. The genome of the organism was sequenced and analysed in order to better understand this whole cell biocatalyst. RESULTS: The genome of R. rhodochrous ATCC BAA-870 is the first Rhodococcus genome fully sequenced using Nanopore sequencing. The circular genome contains 5.9 megabase pairs (Mbp) and includes a 0.53 Mbp linear plasmid, that together encode 7548 predicted protein sequences according to BASys annotation, and 5535 predicted protein sequences according to RAST annotation. The genome contains numerous oxidoreductases, 15 identified antibiotic and secondary metabolite gene clusters, several terpene and nonribosomal peptide synthetase clusters, as well as 6 putative clusters of unknown type. The 0.53 Mbp plasmid encodes 677 predicted genes and contains the nitrile converting gene cluster, including a nitrilase, a low molecular weight nitrile hydratase, and an enantioselective amidase. Although there are fewer biotechnologically relevant enzymes compared to those found in rhodococci with larger genomes, such as the well-known Rhodococcus jostii RHA1, the abundance of transporters in combination with the myriad of enzymes found in strain BAA-870 might make it more suitable for use in industrially relevant processes than other rhodococci. CONCLUSIONS: The sequence and comprehensive description of the R. rhodochrous ATCC BAA-870 genome will facilitate the additional exploitation of rhodococci for biotechnological applications, as well as enable further characterisation of this model organism. The genome encodes a wide range of enzymes, many with unknown substrate specificities supporting potential applications in biotechnology, including nitrilases, nitrile hydratase, monooxygenases, cytochrome P450s, reductases, proteases, lipases, and transaminases.BT/Industrial MicrobiologyBT/Biocatalysi