Journal:

Article Title: Annotations and Functional Analyses of the Rice WRKY Gene Superfamily Reveal Positive and Negative Regulators of Abscisic Acid Signaling in Aleurone Cells 1 [w]

doi: 10.1104/pp.104.054312

Figure Lengend Snippet: Chromosomal distribution of OsWRKY Genes. A, The distribution of OsWRKY genes in the rice genome. The chromosomal information for OsWRKY genes identified in the japonica genome was determined based on BAC information obtained from the NCBI (http://www.ncbi.nlm.nih.gov). To determine chromosomal information for genes identified in the indica genome, the corresponding contig sequences were used for BLAST search against the japonica BAC sequences in the NCBI. The overlapped sequences were determined based on BLAST results, and the chromosomal information on these genes was obtained from the overlapped japonica BAC information. Detailed results were listed in Supplemental Table V. The information on the length of rice chromosomes was obtained from the IRGSP (http://rgp.dna.affrc.go.jp/IRGSP/). B, Chromosomal locations of OsWRKY genes in rice chromosome 1. Six regions (A–F) with a higher density of OsWRKY genes were revealed. Possible duplicated OsWRKY genes are highlighted in gray.

Article Snippet: About 361 Mb of rice indica contig sequences were downloaded from Beijing Genomics Institute (BGI; http://btn.genomics.org.cn/rice ), which covers about 90% of the rice genome.

Techniques:

Journal: bioRxiv

Article Title: Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

doi: 10.1101/2020.09.29.318477

Figure Lengend Snippet: The pipeline for obtaining superior-quality genome assemblies for malaria mosquitoes based on Hi-C scaffolding of Oxford Nanopore sequencing contigs.

Article Snippet: To maximize the use of the data, tools, and workflows of this study, we present a pipeline for obtaining superior-quality genome assemblies for malaria mosquitoes based on Hi-C scaffolding of Oxford Nanopore sequencing contigs ( ).

Techniques: Hi-C, Scaffolding, Nanopore Sequencing

Journal: Journal of Antimicrobial Chemotherapy

Article Title: Tn 1546 is part of a larger plasmid-encoded genetic unit horizontally disseminated among clonal Enterococcus faecium lineages

doi: 10.1093/jac/dkq219

Figure Lengend Snippet: Genetic map of pIP816 and pVEF4. Coding regions are represented by arrows indicating the direction of transcription and are coloured according to their predicted functions. The inverted repeats (IR) of the Tn 1546 transposon and the predicted origin of replication ( oriR ) of the plasmids are given as black boxes. The group II intron En . fm .I2 of pVEF4 is shown as dark grey boxes flanking the intron-encoding protein. Thin arrows indicate the 25 kb larger genetic unit. Truncated CDSs are indicated with a prime symbol (e.g. tnp ′).

Article Snippet: The draft contig sequences of pVEF4 were provided by Macrogen, Korea, using BigDye chemistry and with a sequence depth of >14× coverage.

Techniques:

Journal: Journal of Antimicrobial Chemotherapy

Article Title: Tn 1546 is part of a larger plasmid-encoded genetic unit horizontally disseminated among clonal Enterococcus faecium lineages

doi: 10.1093/jac/dkq219

Figure Lengend Snippet: Coding sequences (CDSs) of the vanA plasmid pVEF4 (partial)

Article Snippet: The draft contig sequences of pVEF4 were provided by Macrogen, Korea, using BigDye chemistry and with a sequence depth of >14× coverage.

Techniques: Plasmid Preparation, Reverse Transcription, Infection

Journal: Journal of Antimicrobial Chemotherapy

Article Title: Tn 1546 is part of a larger plasmid-encoded genetic unit horizontally disseminated among clonal Enterococcus faecium lineages

doi: 10.1093/jac/dkq219

Figure Lengend Snippet: Structural features of En . fm .I2 and its intron-encoded protein (IEP). (a) Predicted secondary RNA structure of En . fm .I2. Intron nucleotides are written in capital letters and exon sequences are written in lowercase letters. Roman numerals denote the domains I–VI. The IEP is found in domain IV. Intron-binding sites (IBSs) 1 and 2 along with the exon-binding sites (EBSs) 1 and 2 are marked by arrows and boxes, respectively. IBS/EBS3 is a single nucleotide interaction and denoted by pointing arrows. The bulged A (branch site) is located in domain VI and shown in bold. (b) The putative IEP displays a reverse transcriptase (RT) domain (bold letters), a maturase (X) domain (italics) and an endonuclease (En) domain (grey). All introns analysed, except two, had identical amino acid composition to En . fm .I2 of pVEF4 (no. 54, top). The non-synonymous substitutions in En . fm .I2 from E. faecium strains 31/F01/H (no. 49) and TUH32-79 (no. 45) are shown in the alignment (identical amino acids are represented by a dot; a dash indicates gaps or substitutions).

Article Snippet: The draft contig sequences of pVEF4 were provided by Macrogen, Korea, using BigDye chemistry and with a sequence depth of >14× coverage.

Techniques: Binding Assay, Reverse Transcription

Journal: Journal of Antimicrobial Chemotherapy

Article Title: Tn 1546 is part of a larger plasmid-encoded genetic unit horizontally disseminated among clonal Enterococcus faecium lineages

doi: 10.1093/jac/dkq219

Figure Lengend Snippet: RT–PCR analyses of the topoisomerase, intron, intron splicing products and enterococcal elongation factor. RT–PCR products from pVEF4 and pVEF3 are given on alternate lanes 1–10. PCR products are shown as follows: topo mRNA without intron (lanes 1 and 2, primer pair ip3F/giiR7); 5′ intron–exon junction (lanes 3 and 4, primer pair ip3F/giiR8); 3′ intron–exon junction (lanes 5 and 6, primer pair giiF5/giiR7); intron lariat structure (lanes 7 and 8, primer pair giiF5/giiR8); and positive RT–PCR control (lanes 9 and 10, primer pair Ent1/Ent2). Ladder (lanes L), 100 bp DNA molecular size marker from New England Biolabs. The sequence data of the ligated exon with the indicated splice site is shown in the lower half of the figure.

Article Snippet: The draft contig sequences of pVEF4 were provided by Macrogen, Korea, using BigDye chemistry and with a sequence depth of >14× coverage.

Techniques: Reverse Transcription Polymerase Chain Reaction, Control, Marker, Sequencing