scholarly journals Full-length-enriched cDNA libraries from Echinococcus granulosus contain separate populations of oligo-capped and trans-spliced transcripts and a high level of predicted signal peptide sequences

2002 ◽  
Vol 122 (2) ◽  
pp. 171-180 ◽  
Author(s):  
Cecilia Fernández ◽  
William F Gregory ◽  
P'ng Loke ◽  
Rick M Maizels
Keyword(s):  
Echinococcus Granulosus ◽  
Signal Peptide ◽  
Full Length ◽  
Cdna Libraries ◽  
Predicted Signal Peptide ◽  
High Level

scholarly journals Serum Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APEX1) Level as a Potential Biomarker of Cholangiocarcinoma

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 413 ◽  
Author(s):  
Doungdean Tummanatsakun ◽  
Tanakorn Proungvitaya ◽  
Sittiruk Roytrakul ◽  
Temduang Limpaiboon ◽  
Sopit Wongkham ◽  
...  
Keyword(s):  
Signal Peptide ◽  
Transmembrane Helix ◽  
Control Group ◽  
Cleavage Sites ◽  
Dot Blot ◽  
Peptide Cleavage ◽  
Potential Biomarker ◽  
Predicted Signal Peptide ◽  
Healthy Control ◽  
Dot Blot Analysis

Diagnostic and/or prognostic biomarkers for cholangiocarcinoma (CCA) are still insufficient with poor prognosis of patients. To discover a new CCA biomarker, we constructed our secretome database of three CCA cell lines and one control cholangiocyte cell line using GeLC-MS/MS. We selected candidate proteins by five bioinformatics tools for secretome analysis. The inclusion criteria were as follows: having predicted signal peptide or being predicted as non-classically secreted protein; together with having no transmembrane helix and being previously detected in plasma and having the highest number of signal peptide cleavage sites. Eventually, apurinic/apyrimidinic endodeoxyribonuclease 1 (APEX1) was selected for further analysis. To validate APEX1 as a bio-marker for CCA, serum APEX1 levels of 80, 39, and 40 samples collected from CCA, benign biliary diseases (BBD), and healthy control groups, respectively, were measured using dot blot analysis. The results showed that serum APEX1 level in CCA group was significantly higher than that in BBD or healthy control group. Among CCA patients, serum APEX1 level was significantly higher in patients having metastasis than in those without metastasis. The higher level of serum APEX1 was correlated with the shorter survival time of the patients. Serum APEX1 level might be a diagnostic and prognostic biomarker for CCA.

scholarly journals Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Christian Clepet ◽  
Tarek Joobeur ◽  
Yi Zheng ◽  
Delphine Jublot ◽  
Mingyun Huang ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Full Length ◽  
Cdna Libraries ◽  
Expressed Sequence

Using inexpensive substrate to achieve high-level lipase A secretion by Bacillus subtilis through signal peptide and promoter screening

2020 ◽  
Vol 99 ◽  
pp. 202-210
Author(s):  
Fengyi Wu ◽  
Jiayuan Ma ◽  
Yaping Cha ◽  
Delin Lu ◽  
Zhiwei Li ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Signal Peptide ◽  
Lipase A ◽  
High Level

Analysis of expressed sequence tags from the ectoparasitic nematode Xiphinema index

Nematology ◽  
2005 ◽  
Vol 7 (1) ◽  
pp. 95-104 ◽  
Author(s):  
Cleber Furlanetto ◽  
Linda Cardle ◽  
Derek J.F. Brown ◽  
John T. Jones
Keyword(s):  
Expressed Sequence Tag ◽  
In Situ Hybridisation ◽  
Cdna Libraries ◽  
Small Scale ◽  
Xiphinema Index ◽  
Genes Encoding ◽  
Predicted Signal Peptide ◽  
Basal Bulb ◽  
Expressed Sequence

AbstractWe report the results of a small-scale expressed sequence tag project performed on the ectoparasitic nematode Xiphinema index. Approximately 1400 genes were sequenced, 70% from a cDNA library generated from dissected basal bulbs (containing the pharyngeal gland cells) and 30% from cDNA libraries generated from whole mixed stage nematodes. A large portion of the bulb library (48%) was composed of proteins with no matches in the database. Further analysis of these genes revealed that a total of 51 contigs were present, half of which encoded novel secreted proteins. By contrast, the whole nematode library contained more housekeeping and nematode-specific genes. Only one of the novel genes from the whole nematode library had a predicted signal peptide at the N-terminus. Genes encoding transthyretin-like proteins were abundant in the bulb library and in situ hybridisation confirmed that one of these is expressed in the basal bulb. Genes encoding a variety of proteases, which were shown using in situ hybridisation to be expressed in the gut, were also identified.

EST-SSR markers derived from an elite barley cultivar (Hordeum vulgare L. ‘Morex’): polymorphism and genetic marker potential

Genome ◽  
2009 ◽  
Vol 52 (8) ◽  
pp. 665-676 ◽  
Author(s):  
Livinus C. Emebiri
Keyword(s):  
Hordeum Vulgare ◽  
Ssr Markers ◽  
Cellulose Synthase ◽  
Cdna Libraries ◽  
Functional Markers ◽  
Hordeum Vulgare L ◽  
Glucanase Activity ◽  
Phenotypic Data ◽  
Trait Locus ◽  
High Level

Microsatellites or simple sequence repeats have become the markers of choice for marker-assisted selection because of their low template DNA requirement, high reproducibility, and high level of polymorphism. This study investigated a new set of barley ( Hordeum vulgare L.) EST-derived SSR markers designed to target gene sequences expressed during grain development, as they are more likely to be important in determining grain quality. The EST sequences (HVSMEh and HVSMEi) were derived from cDNA libraries of the elite six-rowed cultivar Morex, made from spikes harvested at 5 to 45 days after pollination. Approximately half of the 110 SSR markers derived from the ESTs were polymorphic in a panel of 8 diverse barley genotypes, with PIC values between 0.19 and 0.79. Twenty of the new markers were mapped to chromosomal locations using 2 doubled haploid populations. To demonstrate marker potential, quantitative trait locus (QTL) analyses were carried out with phenotypic data on wort β-glucan content and β-glucanase activity, two traits with a long history of genetic studies. Most of the EST-SSR markers mapped to within 10 cM of the cellulose synthase (HvCesA) and cellulose synthase-like (HvCslF) genes, which provides highly informative functional markers for tracking these genes in breeding programs. It was also observed that on any given chromosome, the QTL for β-glucan content and β-glucanase activity were rarely coincident but tended to occur in adjacent intervals along chromosomal regions, which agreed with their independent genetic basis; the adjacent localization may be important for coordination of cell wall degradation during germination and malting.

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