Journal:

Article Title: Dynamic Partitioning into Lipid Rafts Controls the Endo-Exocytic Cycle of the ?L/? 2 Integrin, LFA-1, during Leukocyte Chemotaxis D⃞

doi: 10.1091/mbc.E05-05-0413

Figure Lengend Snippet: Ratiometric analysis of αL/β 2 enrichment in ruffles

Article Snippet: Cells were then inspected with a laser scanning confocal microscope MRC-1024 (Bio-Rad, Hercules, CA), and the distribution analysis was performed as indicated in legend. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 αL-GFP/β 2 WGA-TRITC αL-GFP/β 2 + Rab11 wt a 11.7 ± 4.8 b 1.8 ± 0.3 αL-GFP/β 2 + Rab11 S25N 6.4 ± 3.2 1.9 ± 0.7 Open in a separate window a HAfpR-CHO cells were transiently cotransfected with αL-GFP/β 2 and either Rab11 wt or Rab11 S25N constructs.

Techniques:

Journal:

Article Title: Dynamic Partitioning into Lipid Rafts Controls the Endo-Exocytic Cycle of the ?L/? 2 Integrin, LFA-1, during Leukocyte Chemotaxis D⃞

doi: 10.1091/mbc.E05-05-0413

Figure Lengend Snippet: Confocal microscopy analysis of fMLF-induced endosomal localization of αL/β2 in PMN. Primary PMN were labeled at 4°C with a Fab′ fragment of an anti-αL mAb, followed by fMLF stimulation and incubation for the indicated time points. Cells were then fixed, permeabilized, and stained with a Cy3-conjugated goat anti-mouse immunoglobulin antiserum (left). Endogenous Rab11 was detected with an affinity-purified rabbit antiserum followed by an FITC-conjugated goat anti-rabbit antibody (top and middle center panels). Endogenous LAMP-1 was detected with an anti-LAMP-1 mAb (IgG2b) followed by a FITC-conjugated, isotype-specific antiserum (bottom center). Nuclei were detected with Hoechst 33342 (blue fluorescence). Right, merged images.

Article Snippet: Cells were then inspected with a laser scanning confocal microscope MRC-1024 (Bio-Rad, Hercules, CA), and the distribution analysis was performed as indicated in legend. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 αL-GFP/β 2 WGA-TRITC αL-GFP/β 2 + Rab11 wt a 11.7 ± 4.8 b 1.8 ± 0.3 αL-GFP/β 2 + Rab11 S25N 6.4 ± 3.2 1.9 ± 0.7 Open in a separate window a HAfpR-CHO cells were transiently cotransfected with αL-GFP/β 2 and either Rab11 wt or Rab11 S25N constructs.

Techniques: Confocal Microscopy, Labeling, Incubation, Staining, Affinity Purification, Fluorescence

Journal:

Article Title: Dynamic Partitioning into Lipid Rafts Controls the Endo-Exocytic Cycle of the ?L/? 2 Integrin, LFA-1, during Leukocyte Chemotaxis D⃞

doi: 10.1091/mbc.E05-05-0413

Figure Lengend Snippet: αL/β2 is recycled via a Rab11-positive compartment. CHO cells stably expressing the fMLF receptor were transiently transfected with αL/β2-GFP and either a wt or a Rab11S25N mutant, expressed as monomeric DsRed chimeric constructs. Twenty-four hours posttransfection, cells were fixed and inspected by laser scanning confocal microscopy.

Article Snippet: Cells were then inspected with a laser scanning confocal microscope MRC-1024 (Bio-Rad, Hercules, CA), and the distribution analysis was performed as indicated in legend. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 αL-GFP/β 2 WGA-TRITC αL-GFP/β 2 + Rab11 wt a 11.7 ± 4.8 b 1.8 ± 0.3 αL-GFP/β 2 + Rab11 S25N 6.4 ± 3.2 1.9 ± 0.7 Open in a separate window a HAfpR-CHO cells were transiently cotransfected with αL-GFP/β 2 and either Rab11 wt or Rab11 S25N constructs.

Techniques: Stable Transfection, Expressing, Transfection, Mutagenesis, Construct, Confocal Microscopy

Journal:

Article Title: Fingerprinting of Bacillus thuringiensis Type Strains and Isolates by Using Bacillus cereus Group-Specific Repetitive Extragenic Palindromic Sequence-Based PCR Analysis

doi: 10.1128/AEM.71.3.1346-1355.2005

Figure Lengend Snippet: Frequency of the Bc-REP and designed primer sequences in five reported genomes of the B. cereus group a

Article Snippet: No further significant matches were found in all the genomes and nucleotide sequences available at the EMBL and NCBI gene banks, including the poorly sequenced B. mycoides (see below). table ft1 table-wrap mode="anchored" t5 TABLE 3. caption a7 Frequency Genome Bc1 Bc2 Bc3 Ba1 Ba2 Bt Bc-REP 100% 28 58 15 14 14 15 Bc-REP 96% 24 18 6 6 6 8 Direct 89 94 32 28 28 33 Reverse 37 71 20 18 18 19 Open in a separate window a Bc1, B. cereus ATCC 14579 genome (NC 004722.1); Bc2, B. cereus ATCC 10987 genome (NC 003909.8); Bc3, B. cereus ZK genome (NC 006274); Ba1, B. anthracis strain Ames genome (NC 003997.3); Ba2, B. anthracis strain Sterne genome (NC 005945.1); Bt, B. thuringiensis strain 97.27 genome (NC 005957.1); Bc-REP 100%, frequency of sequences showing 100% homology with Bc-REP; Bc-REP 96%, frequency of sequences showing 96% homology with Bc-REP; Direct, frequency of sequences showing 100% homology with the designed direct primer; Reverse, frequency of sequences showing 100% homology with the designed reverse primer.

Techniques:

Journal: Applied nursing research : ANR

Article Title: Animal Models in Genomic Research: Techniques, Applications, and Roles for Nurses

doi: 10.1016/j.apnr.2016.07.016

Figure Lengend Snippet: Resources

Article Snippet: Resources for appropriate selection of a model, strain, and substrain are described later ( ). table ft1 table-wrap mode="anchored" t5 caption a7 Resource Name Sponsor/Source Description URL Mouse Genome Informatics The Jackson Laboratory with data contributed form several well-known research groups International database providing a wealth of data (e.g. genetic, genomic, biological, phenotypic) about laboratory mice used in biomedical research.

Techniques: Sequencing, Variant Assay, Knock-Out, Functional Assay, Produced, Generated, Mutagenesis

Journal: Acta Crystallographica. Section F, Structural Biology Communications

Article Title: Full-length nisin immunity protein NisI from Lactococcus lactis in a lipid-free form: crystallization and X-ray analysis

doi: 10.1107/S2053230X17008214

Figure Lengend Snippet: Macromolecule-production information

Article Snippet: To quench the methylation reaction, 1 M Tris–HCl pH 8.0 was added to give a concentration of 100 m M . Finally, the sample was further purified using a Superdex 200 pg 26/600 column (GE Healthcare) equilibrated with 10 m M Tris–HCl pH 8.0, 50 m M NaCl, 2 m M β-mercaptoethanol. table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 Source organism L. lactis subsp. lactis ATCC 11454 DNA source Genomic DNA Forward primer † 5′-CGATAC CATATG CAAACAAGTCATAAAAAGGTGAGG-3′ Reverse primer † 5′-G GAATTC ACTCGAGGTTTCCTACCTTCGTTGCAAGC-3′ Cloning vector pSKB3 (modified pET-28a) Expression vector pSKB3 (modified pET-28a) Expression host E. coli BL21 (DE3) Star Complete amino-acid sequence of the construct produced ‡ MGSSHHHHHHDYDIPTTENLYFQGHM QTSHKKVRFDEGSYTNFIYDNKSYFVTDKEIPQENVNNSKVKFYKLLIVDMKSEKLLSSSNKNSVTLVLNNIYEASDKSLCMGINDRYYKILPESDKGAVKALRLQNFDVTSDISDDNFVIDKNDSRKIDYMGNIYSISDTTVSDEELGEYQDVLAEVRVFDSVSGKSIPRSEWGRIDKDGSNSKQSRTEWDYGEIHSIRGKSLTEAFAVEINDDFKLATKVGN LE Open in a separate window † Restriction sites are underlined.

Techniques: Cloning, Plasmid Preparation, Modification, Expressing, Sequencing, Construct, Produced

Journal: Turkish Journal of Biology

Article Title: hsa-miR-301a- and SOX10-dependent miRNA-TF-mRNA regulatory circuits in breast cancer

doi: 10.3906/biy-1708-17

Figure Lengend Snippet: The characteristics of the datasets.

Article Snippet: As a result, 2 independent mRNA studies and 1 miRNA study including breast tumors and normal samples were selected to be analyzed (Table ). table ft1 table-wrap mode="anchored" t5 Table 1 caption a7 GEO ID Platform Normal samples Tumor samples GSE3744 Affymetrix Human Genome U133 Plus 2.0 Array 7 40 GSE5764 Affymetrix Human Genome U133 Plus 2.0 Array 15 15 GSE45666 Agilent-021827 Human miRNA Microarray G4470C 15 80 GSE17907 (Test data) Affymetrix Human Genome U133 Plus 2.0 Array 4 51 Open in a separate window The characteristics of the datasets.

Techniques: Microarray

Journal: G3: Genes|Genomes|Genetics

Article Title: A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

doi: 10.1093/g3journal/jkab052

Figure Lengend Snippet: Statistical data summary of the USDA_OmykA_1.1 (Arlee) rainbow trout genome assembly

Article Snippet: The total length of the 710 unplaced scaffolds that are not anchored to a chromosome is ∼108 Mb. table ft1 table-wrap mode="anchored" t5 caption a7 Feature Canu contigs Polished contigs BioNano scaffolds Hi-C scaffolds With linkage information Number of sequences 1,591 1,591 1,044 919 938 Total length 2,340,653,759 2,341,478,269 2,341,947,072 2,342,042,072 2,341,652,372 Maximum length 63,126,076 63,163,333 88,429,459 90,526,592 88,429,459 Minimum length 1,061 1,057 16,956 16,956 16,956 N50 9,835,815 9,837,718 28,011,862 47,542,702 39,165,350 L50 58 58 31 17 22 N90 1,125,404 1,125,715 1,804,217 2,489,804 2,487,114 L90 333 333 170 98 116 BUSCO * C: 95.9% (S: 48.3%; D: 47.6%) C: 96.2% (S: 46.2%; D: 50.0%) NA C: 96.4% (S: 46.7%; D: 49.7%) NA Open in a separate window * Benchmarking Universal Single-Copy Orthologs.

Techniques:

Journal: The Plant Cell

Article Title: Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping ^[OPEN]

doi: 10.1105/tpc.17.00514

Figure Lengend Snippet: Recent Results of Physical Maps Aligned to Their Respective Reference Genomes

Article Snippet: Some genomic regions are easily corrected, others require multiple iterations to untangle and resolve discrepancies , and others will likely remain unresolved and may require local reassembly of the underlying DNA sequence. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 3. caption a7 Sequence Contigs from G. herbaceum Chromosome 4 Ordered and Oriented into Pseudomolecules by the Hi-C Methodology (as Assembled by PhaseGenomics). (A) The first row is a colored bar that represents the concatenated contigs based on clustering and orientation likelihood ratios of Hi-C data.

Techniques: Sequencing

Journal: The Plant Cell

Article Title: Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping ^[OPEN]

doi: 10.1105/tpc.17.00514

Figure Lengend Snippet: An Illustration of Bionano Contigs Likely Spanning Centromeric Regions in the G. herbaceum Reference.

Article Snippet: Some genomic regions are easily corrected, others require multiple iterations to untangle and resolve discrepancies , and others will likely remain unresolved and may require local reassembly of the underlying DNA sequence. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 3. caption a7 Sequence Contigs from G. herbaceum Chromosome 4 Ordered and Oriented into Pseudomolecules by the Hi-C Methodology (as Assembled by PhaseGenomics). (A) The first row is a colored bar that represents the concatenated contigs based on clustering and orientation likelihood ratios of Hi-C data.

Techniques:

Journal: The Plant Cell

Article Title: Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping ^[OPEN]

doi: 10.1105/tpc.17.00514

Figure Lengend Snippet: Sequence Contigs from G. herbaceum Chromosome 4 Ordered and Oriented into Pseudomolecules by the Hi-C Methodology (as Assembled by PhaseGenomics).

Article Snippet: Some genomic regions are easily corrected, others require multiple iterations to untangle and resolve discrepancies , and others will likely remain unresolved and may require local reassembly of the underlying DNA sequence. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 3. caption a7 Sequence Contigs from G. herbaceum Chromosome 4 Ordered and Oriented into Pseudomolecules by the Hi-C Methodology (as Assembled by PhaseGenomics). (A) The first row is a colored bar that represents the concatenated contigs based on clustering and orientation likelihood ratios of Hi-C data.

Techniques: Sequencing, Hi-C

Journal: Heredity

Article Title: From next-generation resequencing reads to a high-quality variant data set

doi: 10.1038/hdy.2016.102

Figure Lengend Snippet: Characteristics of several commercially available NGS platforms

Article Snippet: Thereby, the large amount of data with shorter read lengths, higher per-base error rates and nonuniform coverage, together with platform-specific read error profiles and artifacts , imposes several statistical and computational challenges in the reliable detection of variants from NGS data ( Harismendy et al. , 2009 ). table ft1 table-wrap mode="anchored" t5 caption a7 Capillary Next generation Sanger 454 Illumina Ion Torrent Platform 3730xl GS FLX+ GS Jr. a HiSeq X Ten HiSeq 2500 MiSeq a PGM 318 a Template preparation Plasmid/PCR emPCR emPCR Solid phase Solid phase Solid phase emPCR Run time ~3 h ~1 Day ~10 h ~3 Days ~6 Days ~65 h ~4–7 h Output/run 0.08 Mb 700 Mb 35 Mb 1.8 Tb 1 Tb 15 Gb 2 Gb Read length 1 kb 1 kb 700 b 2 × 150 b 2 × 125 b 2 × 300 b 400 b No. of reads/run 96 (standard) up to 384 (rare) 1 M 0.1 M 6 B 4 B 25 M 5.5 M Error rate b 0.1–1% ~1% ~1% ~0.1% ~0.1% ~0.1% ~1% Primary errors Substitutions Indels Substitutions c Indels Advantages • Long reads • High quality • Long reads • Fast run time • Highest throughput • Low per-base cost • Unmodified nucleotides • No optical scanning necessary, and thus no photo damage • Fast run time Limitations • Low throughput • High costs • High error rates in homopolymer regions • Low throughput • High costs • Cumbersome emPCR • Short reads • Random dispersion of clusters can cause poor sequence quality • Underrepresentation of AT-rich and GC-rich regions • High error rates in homopolymer regions • Cumbersome emPCR Open in a separate window Abbreviations: emPCR, emulsion PCR; NGS, next-generation sequencing.

Techniques: Plasmid Preparation, Sequencing