Journal: Biotechnology for Biofuels

Article Title: A novel fungal GH30 xylanase with xylobiohydrolase auxiliary activity

doi: 10.1186/s13068-019-1455-2

Figure Lengend Snippet: Identity and similarity values among the amino acid sequences of the mature xylanase Tt Xyn30A and other mature GH30 xylanases from different microorganisms (carbohydrate binding domains or dockerins are not included)

Article Snippet: The gene coding for the putative protein Tt Xyn30A (Protein ID 38558; chromosome 1: 7956351–7958140; accession no. XP_003660270.1), designated ex30a , was synthesized as codon optimized for expression in P. pastoris host strain X-33 and was cloned in vector pEX-K4 by GenScript (Piscataway, NJ, USA).

Techniques: Binding Assay

Journal: Biotechnology for Biofuels

Article Title: A novel fungal GH30 xylanase with xylobiohydrolase auxiliary activity

doi: 10.1186/s13068-019-1455-2

Figure Lengend Snippet: SDS-PAGE ( a ) and IEF ( b ) of Tt Xyn30A. a LMW standard protein markers (1), purified Tt Xyn30A (2), and Tt Xyn30A after enzymatic treatment with EndoH (3). b Purified Tt Xyn30A (4), standard protein markers with p I range 3.0–10.0 (5), and Tt Xyn30A after enzymatic treatment with EndoH (6)

Article Snippet: The gene coding for the putative protein Tt Xyn30A (Protein ID 38558; chromosome 1: 7956351–7958140; accession no. XP_003660270.1), designated ex30a , was synthesized as codon optimized for expression in P. pastoris host strain X-33 and was cloned in vector pEX-K4 by GenScript (Piscataway, NJ, USA).

Techniques: SDS Page, Purification

Journal: Biotechnology for Biofuels

Article Title: A novel fungal GH30 xylanase with xylobiohydrolase auxiliary activity

doi: 10.1186/s13068-019-1455-2

Figure Lengend Snippet: TLC analysis of hydrolysis products from beechwood xylan by recombinant Tt Xyn30A. The reaction was carried out in 0.05 mM citrate–phosphate buffer pH 4.0 at 50 °C. The substrate and enzyme loadings were 5 mg mL −1 and 0.09 U mL −1 , respectively. Xylooligosaccharides (DP 2–6) and aldouronic acids (aldotetrauronic and aldopentauronic acid) were used as standards

Article Snippet: The gene coding for the putative protein Tt Xyn30A (Protein ID 38558; chromosome 1: 7956351–7958140; accession no. XP_003660270.1), designated ex30a , was synthesized as codon optimized for expression in P. pastoris host strain X-33 and was cloned in vector pEX-K4 by GenScript (Piscataway, NJ, USA).

Techniques: Recombinant

Journal: Biotechnology for Biofuels

Article Title: A novel fungal GH30 xylanase with xylobiohydrolase auxiliary activity

doi: 10.1186/s13068-019-1455-2

Figure Lengend Snippet: Time course of the hydrolysis products of beechwood glucuronoxylan under the action of the recombinant Tt Xyn30A by HPAEC-PAD. The reaction was carried out in 0.05 mM citrate–phosphate buffer pH 4.0 at 50 °C. The substrate and enzyme loadings were 5 mg mL −1 and 0.09 U mL −1 , respectively

Article Snippet: The gene coding for the putative protein Tt Xyn30A (Protein ID 38558; chromosome 1: 7956351–7958140; accession no. XP_003660270.1), designated ex30a , was synthesized as codon optimized for expression in P. pastoris host strain X-33 and was cloned in vector pEX-K4 by GenScript (Piscataway, NJ, USA).

Techniques: Recombinant

Journal: Biotechnology for Biofuels

Article Title: A novel fungal GH30 xylanase with xylobiohydrolase auxiliary activity

doi: 10.1186/s13068-019-1455-2

Figure Lengend Snippet: Analysis of the hydrolysis products from xylooligosaccharides (X3–X6) using HPAEC-PAD under the action of Tt Xyn30A. The reactions were carried out in 0.05 mM citrate–phosphate buffer pH 4.0 at 50 °C for 18 h, and the enzyme loading was 0.09 U mL −1

Article Snippet: The gene coding for the putative protein Tt Xyn30A (Protein ID 38558; chromosome 1: 7956351–7958140; accession no. XP_003660270.1), designated ex30a , was synthesized as codon optimized for expression in P. pastoris host strain X-33 and was cloned in vector pEX-K4 by GenScript (Piscataway, NJ, USA).

Techniques:

Journal: Biotechnology for Biofuels

Article Title: A novel fungal GH30 xylanase with xylobiohydrolase auxiliary activity

doi: 10.1186/s13068-019-1455-2

Figure Lengend Snippet: Suggested mode of action of Tt Xyn30A against beechwood glucuronoxylan ( a ) and schematic presentation of products liberated from the exo-action of Tt Xyn30A against UXOS ( b ). The red arrows indicate the endo-action of the enzyme against the substituted polysaccharide leading to the formation of UXOS. The green arrow indicates the exo-action of the enzyme against the liberated UXOS, while the yellow arrow indicates the direction of the exo-action from the non-reducing end to the reducing end

Article Snippet: The gene coding for the putative protein Tt Xyn30A (Protein ID 38558; chromosome 1: 7956351–7958140; accession no. XP_003660270.1), designated ex30a , was synthesized as codon optimized for expression in P. pastoris host strain X-33 and was cloned in vector pEX-K4 by GenScript (Piscataway, NJ, USA).

Techniques:

Journal: Biotechnology for Biofuels

Article Title: A novel fungal GH30 xylanase with xylobiohydrolase auxiliary activity

doi: 10.1186/s13068-019-1455-2

Figure Lengend Snippet: Sequence alignment of Tt Xyn30A and other GH30 xylanases, either of bacterial or fungal origin. The R46 residue (as in Xyn30B) is indicated by a blue arrow . Red arrows indicate the strictly conserved catalytic glutamate residues. The residue R293 of E. chrysanthemi XynA is indicated by a green arrow . The identical residues are shown in white on a red background , while similar residues are shown in red on a white background . Talaromyces cellulolyticus Xyn30B (GAM36763), Aeromonas caviae XynD (AAB63573.1), Bacillus sp. BP7 Xyn5B (ADM15019.1), Bacillus subtilis Bs XynC (CAA97612.1), Clostridium thermocellum Ct Xyn30A (ABN54208.1), Clostridium papyrosolvens Cp Xyn30A (EGD48159.1), Erwinia chrysanthemi XynA (AAB53151.1), Paenibacillus barcinonensis Xyn30D (AEY82463.1), Bispora sp. MEY-1 XylD (ADG62369.1), Penicillium purpurogenum XynC (AKH40280), Trichoderma reesei XYN IV (AAP64786.1), Trichoderma reesei XYN VI (G0RV92)

Article Snippet: The gene coding for the putative protein Tt Xyn30A (Protein ID 38558; chromosome 1: 7956351–7958140; accession no. XP_003660270.1), designated ex30a , was synthesized as codon optimized for expression in P. pastoris host strain X-33 and was cloned in vector pEX-K4 by GenScript (Piscataway, NJ, USA).

Techniques: Sequencing, Residue

Journal: Radiation research

Article Title: Chromosome Translocations, Inversions and Telomere Length for Retrospective Biodosimetry on Exposed U.S. Atomic Veterans

doi: 10.1667/RR15240.1

Figure Lengend Snippet: Directional genomic hybridization (dGH). Representative images of metaphase spreads labeled with dGH whole chromosome 1, 2 and 3 paints (red) and counter stained with DAPI (blue). Panel A: A normal metaphase spread free of any structural rearrangements. dGH chromosome paints uniformly label a single sister chromatid of a chromosome. Panel B: An inversion (double signal switch; yellow arrow) on chromosome 2. Panel C: Translocation involving chromosome 3 and a second, unpainted chromosome (white arrows).

Article Snippet: Directional Genomic Hybridization and Imaging To simultaneously identify translocations and inversions, single-color whole chromosome 1, 2 and 3 dGH paints (KromaTiD Inc., Ft. Collins, CO) were used as previously described ( 21 , 29 ).

Techniques: Hybridization, Labeling, Staining, Translocation Assay

Journal: Genome Research

Article Title: Genomic loci susceptible to systematic sequencing bias in clinical whole genomes

doi: 10.1101/gr.255349.119

Figure Lengend Snippet: Suspect loci in detected variants of a gold-standard genome. Distribution of allelic fractions of SNVs called in Chromosome 1 of NA12878, classified as either suspect SNVs ( top row in A – C ) in data set 1 (Personalis), or nonsuspect SNVs (second row in D – F ). SNVs were also classified based on whether they matched the NIST GIAB v3.3.2 benchmark variants ( left column), did not match the benchmark variants ( middle column), or were outside of the GIAB benchmark region ( right column). Low coverage variants (<10 supporting reads) were excluded from this analysis. ( G ) Cropped panels from the Integrative Genomics Viewer , highlighting suspect loci from data set 1 in Chromosome 1 that were called as variants separately in NA12878. NA12878 was sequenced with Illumina HiSeq but not used as part of the patient data set to create the IncDB ( , ). Reads are shown in gray with colored bands where nonreference allelic reads were observed (A = green, C = blue, G = brown, T = red). Suspect SNVs and their respective read proportions in the NA12878 cell line are indicated above ; these systematically occur at similar levels across all patients in the IncDBs used to identify them. ( Left , middle ) Suspect SNVs in exonic and intronic regions of genes in the PanelApp intellectual disability panel . ( Right ) Suspect SNV in an intergenic region.

Article Snippet: In order to confirm that these loci occur independently from the samples examined, specific suspect loci were examined in the reference sample NA12878 cell line, which was sequenced and had variants called by Personalis, Inc. using the same pipeline as data set 1 for comparison but which was not part of any of the data sets used to generate the IncDBs.

Techniques: