Journal: Ecology and Evolution

Article Title: How low can you go? Introducing SeXY: sex identification from low‐quantity sequencing data despite lacking assembled sex chromosomes

doi: 10.1002/ece3.9185

Figure Lengend Snippet: Summary table showing percentage of correct sex determination across tested combinations of reference genome assembly (RefGEN), reference sex‐chromosome assembly (RefX and RefY), and number of mapped reads. Results are shown for the beluga data and the cetacean/cow RefGEN assemblies tested (left columns) and for the polar bear data and the bear/dog RefGEN assemblies tested (right columns). The value below each RefGEN indicates the assembly N50. For cells with two estimates, the left value indicates estimates including both incorrectly determined and undetermined sex, and the right value indicates estimates including incorrectly determined sex only (excluding undetermined sex). Only one value is included if both estimates were the same. Percentages in each cell are based on 10 sample individuals: five females and five males. Sex determination for each indvidual was calculated using the average value of 10 replicates. Individuals were determined as females if their X:A ratio was ≥ 0.8, and as males if their X:A ratio was ≤0.7. We interpreted an X:A ratio of 0.7–0.8 as undetermined sex. Corresponding summary table for tests using HumanX and HumanY as RefX and RefY, respectively, is provided in Table S7 .

Article Snippet: Clear exceptions could be seen when using Beluga v1 (N50 161 kb) and Orca (N50 13 Mb) as RefGEN in the beluga dataset.

Techniques:

Journal:

Article Title: Identification of Novel Helicobacter spp. from a Beluga Whale †

doi: 10.1128/AEM.68.4.2040-2043.2002

Figure Lengend Snippet: PCR primers used in this study

Article Snippet: The sequence for the novel helicobacter beluga fecal culture isolate MIT 00-7128 (ATCC BAA-429) differs from that of helicobacter dolphin isolate MIT 99-5656 by only 4 bp (99.7% similar) and thus appears to represent the same species ( 15 ).

Techniques: Sequencing

Journal:

Article Title: Identification of Novel Helicobacter spp. from a Beluga Whale †

doi: 10.1128/AEM.68.4.2040-2043.2002

Figure Lengend Snippet: Gel electrophoresis with ethidium bromide staining demonstrating 1,200-bp PCR target sequence using Helicobacter-specific primers (arrow). Lane MW, molecular weight standards; lane 1, reagent control; lane 2, Helicobacter-positive control (H. hepaticus); lanes 3 and 4, MIT 00-7125 and MIT 00-7126 (animal 2), representing the beluga feces and gastric fluid, respectively; lanes 5 and 6, MIT 00-7131 and MIT 00-7132 (animal 3), representing the beluga feces and gastric fluid, respectively; lanes 7 and 8, MIT 00-7128 and MIT 00-7129, representing the DNA from beluga (animal 1) feces and gastric fluid, respectively.

Article Snippet: The sequence for the novel helicobacter beluga fecal culture isolate MIT 00-7128 (ATCC BAA-429) differs from that of helicobacter dolphin isolate MIT 99-5656 by only 4 bp (99.7% similar) and thus appears to represent the same species ( 15 ).

Techniques: Nucleic Acid Electrophoresis, Staining, Sequencing, Molecular Weight, Control, Positive Control

Journal:

Article Title: Identification of Novel Helicobacter spp. from a Beluga Whale †

doi: 10.1128/AEM.68.4.2040-2043.2002

Figure Lengend Snippet: Dendrogram depicting the phylogenetic location of the Helicobacter spp. constructed on the basis of 16S rRNA sequence similarity values. The sequences from the beluga whale (isolates MIT 00-7128 and MIT 00-7129) are identified with arrows. The number in parentheses following the MIT accession number is the GenBank accession number. The scale bare is equal to a 2% difference in nucleotide sequences as determined by measuring the lengths of the horizontal lines connecting two species.

Article Snippet: The sequence for the novel helicobacter beluga fecal culture isolate MIT 00-7128 (ATCC BAA-429) differs from that of helicobacter dolphin isolate MIT 99-5656 by only 4 bp (99.7% similar) and thus appears to represent the same species ( 15 ).

Techniques: Construct, Sequencing

Journal:

Article Title: Identification of Novel Helicobacter spp. from a Beluga Whale †

doi: 10.1128/AEM.68.4.2040-2043.2002

Figure Lengend Snippet: PCR-RFLP patterns of the 1,200-bp species-specific Helicobacter PCR product from beluga gastric fluid and feces. Lane MW, molecular weight standards; lane 1, MIT 00-7128 PCR product from beluga fecal isolate digested by HhaI; lane 2, MIT 00-7129 PCR product from beluga gastric fluid digested by HhaI; lane 3, MIT 00-7128 PCR product from beluga fecal isolate digested by AluI; lane 4, MIT 00-7129 PCR product from beluga gastric fluid digested by AluI.

Article Snippet: The sequence for the novel helicobacter beluga fecal culture isolate MIT 00-7128 (ATCC BAA-429) differs from that of helicobacter dolphin isolate MIT 99-5656 by only 4 bp (99.7% similar) and thus appears to represent the same species ( 15 ).

Techniques: Molecular Weight