scholarly journals Evaluation of the performance of different plastics used to seal nylon cDNA arrays

2009 ◽  
Vol 33 (spe) ◽  
pp. 1883-1887
Author(s):  
Antônio Paulino da Costa Netto ◽  
Rodrigo Duarte Drummond ◽  
Juliana de Maria Felix ◽  
Renato Atílio Jorge ◽  
Marcelo Menossi
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Shielding Effect ◽  
Maximum Information ◽  
Polyvinylidene Chloride ◽  
Cdna Arrays ◽  
Plastic Bags ◽  
Data Variability ◽  
Plastic Bag ◽  
High Throughput Gene Expression

cDNA arrays are a powerful tool for discovering gene expression patterns. Nylon arrays have the advantage that they can be re-used several times. A key issue in high throughput gene expression analysis is sensitivity. In the case of nylon arrays, signal detection can be affected by the plastic bags used to keep membranes humid. In this study, we evaluated the effect of five types of plastics on the radioactive transmittance, number of genes with a signal above the background, and data variability. A polyethylene plastic bag 69 μm thick had a strong shielding effect that blocked 68.7% of the radioactive signal. The shielding effect on transmittance decreased the number of detected genes and increased the data variability. Other plastics which were thinner gave better results. Although plastics made from polyvinylidene chloride, polyvinyl chloride (both 13 μm thick) and polyethylene (29 and 7 μm thick) showed different levels of transmittance, they all gave similarly good performances. Polyvinylidene chloride and polyethylene 29 mm thick were the plastics of choice because of their easy handling. For other types of plastics, it is advisable to run a simple check on their performance in order to obtain the maximum information from nylon cDNA arrays.

Evolution of gene expression patterns in a model of branching morphogenesis

1999 ◽  
Vol 277 (4) ◽  
pp. F650-F663 ◽  
Author(s):  
Anna Pavlova ◽  
Robert O. Stuart ◽  
Martin Pohl ◽  
Sanjay K. Nigam
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Expression Patterns ◽  
Branching Morphogenesis ◽  
Computational Method ◽  
Metanephric Mesenchyme ◽  
Ureteric Bud ◽  
Cdna Arrays ◽  
Apoptotic Genes ◽  
Collecting System

Branching morphogenesis of the ureteric bud in response to unknown signals from the metanephric mesenchyme gives rise to the urinary collecting system and, via inductive signals from the ureteric bud, to recruitment of nephrons from undifferentiated mesenchyme. An established cell culture model for this process employs cells of ureteric bud origin (UB) cultured in extracellular matrix and stimulated with conditioned media (BSN-CM) from a metanephric mesenchymal cell line (H. Sakurai, E. J. Barros, T. Tsukamoto, J. Barasch, and S. K. Nigam. Proc. Natl. Acad. Sci. USA 94: 6279–6284, 1997.). In the presence of BSN-CM, the UB cells form branching tubular structures reminiscent of the branching ureteric bud. The pattern of gene regulation in this model of branching morphogenesis of the kidney collecting system was investigated using high-density cDNA arrays. Software and analytical methods were developed for the quantification and clustering of genes. With the use of a computational method termed “vector analysis,” genes were clustered according to the direction and magnitude of differential expression in n-dimensional log-space. Changes in gene expression in response to the BSN-CM consisted primarily of differential expression of transcription factors with previously described roles in morphogenesis, downregulation of pro-apoptotic genes accompanied by upregulation of anti-apoptotic genes, and upregulation of a small group of secreted products including growth factors, cytokines, and extracellular proteinases. Changes in expression are discussed in the context of a general model for epithelial branching morphogenesis. In addition, the cDNA arrays were used to survey expression of epithelial markers and secreted factors in UB and BSN cells, confirming the largely epithelial character of the former and largely mesenchymal character of the later. Specific morphologies (cellular processes, branching multicellular cords, etc.) were shown to correlate with the expression of different, but overlapping, genomic subsets, suggesting differences in morphogenetic mechanisms at these various steps in the evolution of branching tubules.

scholarly journals The expression patterns of HSP70 and HSP90 genes of abalone (Haliotis squamata) using 2-phenoxyethanol as an anaesthetic during transportation

2021 ◽  
Vol 322 ◽  
pp. 04003
Author(s):  
Ngurah S. Yasa ◽  
Lutfi Anshory ◽  
Winarno ◽  
Pande Gde Sasmita Julyantoro
Keyword(s):  
Data Analysis ◽  
Survival Rate ◽  
Confidence Interval ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Paired Sample ◽  
Plastic Bags ◽  
Plastic Bag ◽  
Pvc Pipe

The packaging of abalone (H. squamata) (39.65 ± 0.24 mm TL) for long-term transportation (>8 hours) requires the addition of substances that provide an anesthetic effect so that it could reduce stress and maintain survival rate post transportation without having to repack. The objective was to investigate the expression pattern of HSP70 and HSP90 genes of abalone during transport with the addition of 2-phenoxyethanol. Abalone was packed using a styrofoam box with dimensions (42.5 x 75.5 x 27.5 cm3), containing 2 pcs of 10L Polyethylene (PE) plastic bags. The plastic bag consisted of 2 pcs of 25cm, 4-inch Polyvinyl Chloride (PVC) pipe for abalone attached. Both ends line enclosed with screen net and tied with rubber bands. Abalone density was 50 heads/pipe. Transportation tests were carried out using a dry system and wet system with and without the addition of 2-phenoxyethanol (PK, KK). Data analysis was done by paired sample ttest and ANOVA with a 95% confidence interval. The results showed that the best abalone survival (85%) was obtained in wet transport + 2-phenoxyethanol (PB) (p <0.05) within 24 hours of transportation.

Gene expression patterns in blood predict future severe endpoints in community acquired pneumonia

Pneumologie ◽  
2018 ◽  
Vol 72 (S 01) ◽  
pp. S8-S9
Author(s):  
M Bauer ◽  
H Kirsten ◽  
E Grunow ◽  
P Ahnert ◽  
M Kiehntopf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Community Acquired Pneumonia ◽  
Gene Expression Patterns

Identification of Differentially Expressed Genes Using cDNA-AFLP During Six Days In Vitro Tuberization of Potato

Zuriat ◽  
2015 ◽  
Vol 14 (1) ◽  
Author(s):  
Nono Carsono ◽  
Christian Bachem
Keyword(s):  
Gene Expression ◽  
Developmental Process ◽  
Expression Patterns ◽  
Induction Medium ◽  
In Vitro Tuberization ◽  
Storage Organ ◽  
Developmentally Regulated ◽  
Study Gene Expression ◽  
Differential Pattern

Tuberization in potato is a complex developmental process resulting in the differentiation of stolon into the storage organ, tuber. During tuberization, change in gene expression has been known to occur. To study gene expression during tuberization over the time, in vitro tuberization system provides a suitable tool, due to its synchronous in tuber formation. An early six days axillary bud growing on tuber induction medium is a crucial development since a large number of genes change in their expression patterns during this period. In order to identify, isolate and sequencing the genes which displaying differential pattern between tuberizing and non-tuberizing potato explants during six days in vitro tuberization, cDNA-AFLP fingerprint, method for the visualization of gene expression using cDNA as template which is amplified to generate an RNA-fingerprinting, was used in this experiment. Seventeen primer combinations were chosen based on their expression profile from cDNA-AFLP fingerprint. Forty five TDFs (transcript derived fragment), which displayed differential expressions, were obtained. Tuberizing explants had much more TDFs, which developmentally regulated, than those from non tuberizing explants. Seven TDFs were isolated, cloned and then sequenced. One TDF did not find similarity in the current databases. The nucleotide sequence of TDF F showed best similarity to invertase ezymes from the databases. The homology of six TDFs with known sequences is discussed in this paper.

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