Effect of glgB/GASBD fusion gene expression on increased branching degree of potato starch and changes in physicochemical properties of starch

We studied gene expression profiles in two mouse models of human thyroid carcinoma: the Tg-RET/PTC3 (RP3) and Tg-E7 mice. RP3 fusion gene is the most frequent mutation found in the first wave post-Chernobyl papillary thyroid cancers (PTCs). E7 is an oncoprotein derived from the human papillomavirus 16 responsible for most cervical carcinoma in women. Both transgenic mice develop thyroid hyperplasia followed by solid differentiated carcinoma in older animals. To understand the different steps leading to carcinoma, we analyzed thyroid gene expression in both strains at different ages by microarray technology. Important biological processes were differentially regulated in the two tumor types. In E7 thyroids, cell cycle was the most up-regulated process, an observation consistent with the huge size of these tumors. In RP3 thyroids, contrary to E7 tumors, several human PTC characteristics were observed: overexpression of many immune-related genes, regulation of human PTC markers, up-regulation of EGF-like growth factors and significant regulation of angiogenesis and extracellular matrix remodeling-related genes. However, similarities were incomplete; they did not concern the overall gene expression and were not conserved in old animals. Therefore, RP3 tumors are partial and transient models of human PTC. They constitute a good model, especially in young animals, to study the respective role of the biological processes shared with human PTC and will allow testing drugs targeting these validated variables.

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Effect of Isolation Methods on Physicochemical Properties of Purple-fleshed Sweet Potato Starch

Proceedings of the International Conference of Science, Technology, Engineering, Environmental and Ramification Researches ◽

10.5220/0010079900370041 ◽

2018 ◽

Author(s):

Elisa Julianti ◽

Herla Rusmarilin ◽

. Ridwansyah ◽

Era Yusraini

Keyword(s):

Physicochemical Properties ◽

Sweet Potato ◽

Potato Starch ◽

Isolation Methods ◽

Sweet Potato Starch

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Impact of RNA Extraction and Target Capture Methods on RNA Sequencing Using Formalin-Fixed, Paraffin Embedded Tissues

10.1101/656736 ◽

2019 ◽

Author(s):

Christopher A. Hilker ◽

Aditya V. Bhagwate ◽

Jin Sung Jang ◽

Jeffrey G Meyer ◽

Asha A. Nair ◽

...

Keyword(s):

Gene Expression ◽

Fusion Gene ◽

Rna Extraction ◽

Extraction Methods ◽

Rna Seq ◽

Gene Detection ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Whole Transcriptome ◽

Formalin Fixed

AbstractFormalin fixed paraffin embedded (FFPE) tissues are commonly used biospecimen for clinical diagnosis. However, RNA degradation is extensive when isolated from FFPE blocks making it challenging for whole transcriptome profiling (RNA-seq). Here, we examined RNA isolation methods, quality metrics, and the performance of RNA-seq using different approaches with RNA isolated from FFPE and fresh frozen (FF) tissues. We evaluated FFPE RNA extraction methods using six different tissues and five different methods. The reproducibility and quality of the prepared libraries from these RNAs were assessed by RNA-seq. We next examined the performance and reproducibility of RNA-seq for gene expression profiling with FFPE and FF samples using targeted (Kinome capture) and whole transcriptome capture based sequencing. Finally, we assessed Agilent SureSelect All-Exon V6+UTR capture and the Illumina TruSeq RNA Access protocols for their ability to detect known gene fusions in FFPE RNA samples. Although the overall yield of RNA varied among extraction methods, gene expression profiles generated by RNA-seq were highly correlated (>90%) when the input RNA was of sufficient quality (≥DV200 30%) and quantity (≥ 100 ng). Using gene capture, we observed a linear relationship between gene expression levels for shared genes that were captured using either All-Exon or Kinome kits. Gene expression correlations between the two capture-based approaches were similar using RNA from FFPE and FF samples. However, TruSeq RNA Access protocol provided significantly higher exon and junction reads when compared to the SureSelect All-Exon capture kit and was more sensitive for fusion gene detection. Our study established pre and post library construction QC parameters that are essential to reproducible RNA-seq profiling using FFPE samples. We show that gene capture based NGS sequencing is an efficient and highly reproducible strategy for gene expression measurements as well as fusion gene detection.

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Effects of Hydrothermal Treatments on Physicochemical Properties and In Vitro Digestion of Starch

Food Biophysics ◽

10.1007/s11483-021-09687-7 ◽

2021 ◽

Author(s):

Ishita Chakraborty ◽

Indira Govindaraju ◽

Sintu Rongpipi ◽

Krishna Kishore Mahato ◽

Nirmal Mazumder

Keyword(s):

Physicochemical Properties ◽

Water Solubility ◽

Amylose Content ◽

Potato Starch ◽

Brown Rice ◽

Food Products ◽

Enzymatic Digestion ◽

Diabetic Patients ◽

Degree Of Hydrolysis

AbstractStarchy food items such as rice and potato with high carbohydrate content raise blood sugar. Hence, consuming low glycaemic foods is one tool to keep diabetes under control. In this study, potato and brown rice (Njavara rice) starches were subjected to hydrothermal treatments: heat moisture treatment (HMT) and annealing (ANN) to develop starch-based food products fit for consumption by diabetic patients. The effects of hydrothermal treatments on physicochemical properties and in-vitro enzymatic digestion of starch were determined. It was observed that hydrothermal treatments decreased the swelling power (SP)% and increased the water solubility (WS)% of the native starches. Native potato starch (PSN) showed a high SP of 80.33%, while annealed potato starch (PANN) and heat moisture treated potato starch (PHMT) showed SP reduced to 65.33% and 51.66%, respectively. Similarly, the SP % reduced from 64.33% in native brown rice (BRN) to 44.66% in annealed brown rice (BRANN) and 38.33% in heat moisture treated brown rice (BRHMT). WS % increased from 32.86% in PSN to 36.66% in PANN and 40.66% in PHMT. In BRN, the WS % increased from 14.0% to 14.66% in BRANN and 18.33% in BRHMT. Amylose content increased from 13.23% and 14.56% in PSN and BRN to 16.14% in PANN 17.99% in PHMT, 17.33% in BRANN, and 18.98% in BRHMT. The PSN crystallinity index reduced from 33.49 to 30.50% in PANN and 32.60% in PHMT. At 12 h of enzymatic digestion, it was found that the degree of hydrolysis (DoH) of PHMT (31.66%) and PANN (36.82%) reduced when compared to PSN (41.09%). Similarly, BRHMT exhibited the lowest DoH at 12 h compared to BRANN (29.24%) and BRN (35.48%). This study highlights the importance of hydrothermal treatments on starch in developing low glycaemic index commercial starch-based food products.

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Assessment of the Presence and the Level of BCR-ABL Fusion Gene Expression and Mutational Status in ABL Kinase Domain

Molecular Aspects of Hematologic Malignancies - Principles and Practice ◽

10.1007/978-3-642-29467-9_25 ◽

2012 ◽

pp. 411-428

Author(s):

Sylwia Czekalska ◽

Magdalena Zawada ◽

Izabela Florek

Keyword(s):

Gene Expression ◽

Fusion Gene ◽

Kinase Domain ◽

Abl Kinase ◽

Mutational Status

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