High-quality genome sequence and description of Paenibacillus dakarensis sp. nov.

AbstractStrain FF9T was isolated in Dakar (Senegal) from a blood-culture taken from a 16-month-old child. MALDI-TOF analysis did not allow for identification. After sequencing, strain FF9T exhibited 98.18% similarity with the 16SrRNA sequence of Paenibacillus uliginis. A polyphasic study of phenotypic and genomic analyses showed that strain FF9T is Gram variable, catalase-positive, and presents a genome of 4,569,428 bp (one chromosome but no plasmid) with 4,427genes (4,352 protein-coding and 75 RNA genes (including 3 rRNA operons). The G+C content is 45.7%. On the basis of these genomic and phenotypic data analyses, we propose the creation of Paenibacillus dakarensis strain FF9T

Synthetic approaches to artificial photosynthesis: general discussion

Metals in Catalysis, Biomimetics & Inorganic Material

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

New catalysts for clean technology

The preparation, characterisation and catalytic performance of both bimetallic nanoparticles and chiral homogeneous catalysts anchored along the interior walls of mesoporous silica (MCM-41) are described. The bimetallic nanoparticles are prepared from Ru6Pd6 and Ru6CSn carbonyl clusters and the resulting MCM derivatives are characterised by a number of methods, including EXAFS, FTIR and STEM. The solvent-free hydrogenation of naphthalene and cyclic polyenes using these catalysts are described, with the Ru6CSn based catalyst giving a 90% selectivity for the corresponding monoenes while the Ru6Pd6 produces the fully hydrogenated product in high yield. The homogeneous catalysts 1-[-(R)-1'-2-bis((diphenylphosphino)ferrocenyl]ethyl-N-N'-dimethylethylenediamine palladium dichloride was heterogenised by anchoring along the inside walls of MCM-41. The catalysed reaction between cinnamylacetate and benzylamine was studied and the catalyst produced 51% of the branched chain product possibly with 100%ee

High-quality genome sequencing and description of Dermabacter indicis sp. nov.

Strain FF11T was isolated from the wound on a researcher's finger who had been bitten by a fish (Protopterus annectens) in Senegal. Analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry did not provide any identification, but the 16S rRNA sequence exhibited 97.9% identity with Dermabacter hominis. Phenotypic and genomic analyses demonstrated that strain FF11T is Gram-positive, facultatively anaerobic, nonmotile and non–spore forming; it exhibited a genome of 2 222 902 bp encoding 2074 protein-coding and 50 RNA genes, with a 63.2% G+C content. We consequently proposed the creation of Dermabacter indicis strain FF11T

High-quality genome sequence and description of Chryseobacterium senegalense sp. nov.

Strain FF12T was isolated from the mouth of a West African lungfish (Protopterus annectens) in Senegal. MALDI-TOF-MS did not provide any identification. This strain exhibited a 97.97% 16S rRNA sequence identity with Kaistella flava. Using a polyphasic study including phenotypic and genomic analyses, strain FF12T is Gram-negative, aero-anaerobic, oxidase-positive, non-motile, non-spore-forming, and exhibited a genome of 4,397,629 bp with a G+C content of 35.1% that coded 4,001 protein-coding and 55 RNA genes. On the basis of these data, we propose the creation of Chryseobacterium senegalense strain FF12T

Noncontiguous finished genome sequence and description of Nocardioides massiliensis sp. nov. GD13T

Nocardioides massiliensis sp. nov strain GD13T is the type strain of N. massiliensis sp. nov., a new species within the genus Nocardioides. This strain was isolated from the faeces of a 62-year-old man admitted to intensive care for Guillain-Barré syndrome. Nocardioides massiliensis is a strictly aerobic Gram-positive rod. Herein we describe the features of this bacterium, together with the complete genome sequence and annotation. The 4 006 620 bp long genome contains 4132 protein-coding and 47 RNA genes

Genome sequence and description of Anaerosalibacter massiliensis sp. nov.

Anaerosalibacter massiliensis sp. nov. strain ND1T (= CSUR P762 = DSM 27308) is the type strain of A. massiliensis sp. nov., a new species within the genus Anaerosalibacter. This strain, the genome of which is described here, was isolated from the faecal flora of a 49-year-old healthy Brazilian man. Anaerosalibacter massiliensis is a Gram-positive, obligate anaerobic rod and member of the family Clostridiaceae. With the complete genome sequence and annotation, we describe here the features of this organism. The 3 197 911 bp long genome (one chromosome but no plasmid) contains 3271 protein-coding and 62 RNA genes, including six rRNA genes

Noncontiguous finished genome sequence and description of Planococcus massiliensis sp. nov., a moderately halophilic bacterium isolated from the human gut

We propose the main phenotypic characteristics and the complete genome sequence and annotation of Planococcus massiliensis strain ES2T (= CSUR P1103 = DSM 28915), the type strain of P. massiliensis sp. nov., isolated from a faeces sample collected from a healthy Senegalese man. It is an aerobic, Gram-positive, moderately halophilic, motile and rod-shaped bacterium. The 3 357 017 bp long genome exhibits a G+C content of 46.0% and contains 3357 protein-coding genes and 48 RNA genes

Noncontiguous finished genome sequence and description of Weeksella massiliensis sp. nov.

Strain FF8T (= CSUR P860 = DSM 28259) was isolated in Dakar, Senegal, from the urine of a 65-year-old man with acute cystitis. This strain shows a similarity of sequence of 16S rRNA of 98.38% with Weeksella virosa, and its GenBank accession numbers are HG931340 and CCMH00000000. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis had a poor score, ranging from 1.32 to 1.56, that did not allow identification of the bacterium. Using a polyphasic study made of phenotypic and genomic analyses, strain FF8T was a Gram-negative, aerobic rod and a member of the family Flavobacteriaceae. The sequenced genome is 2 562 781 bp with one chromosome but no plasmid. It exhibits a G + C content of 35.9% and contains 2390 protein-coding and 56 RNA genes, including a complete rRNA operon. On the basis of these data, we propose the creation of Weeksella massiliensis sp. nov