scholarly journals Towards unambiguous transcript mapping in the allotetraploid Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 929-938 ◽  
Author(s):  
Isobel A.P. Parkin ◽  
Wayne E. Clarke ◽  
Christine Sidebottom ◽  
Wentao Zhang ◽  
Stephen J. Robinson ◽  
...  
Keyword(s):  
Brassica Species ◽  
Evolutionary Origins ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Multiple Copies ◽  
Duplication Events ◽  
Cost Efficient ◽  
Well Differentiated ◽  
Expressed Sequence ◽  
Selection Of

The architecture of the Brassica napus genome is marked by its evolutionary origins. The genome of B. napus was formed from the hybridization of two closely related diploid Brassica species, both of which evolved from an hexaploid ancestor. The extensive whole genome duplication events in its near and distant past result in the allotetraploid genome of B. napus maintaining multiple copies of most genes, which predicts a highly complex and redundant transcriptome that can confound any expression analyses. A stringent assembly of 142 399 B. napus expressed sequence tags allowed the development of a well-differentiated set of reference transcripts, which were used as a foundation to assess the efficacy of available tools for identifying and distinguishing transcripts in B. napus ; including microarray hybridization and 3′ anchored sequence tag capture. Microarray platforms cannot distinguish transcripts derived from the two progenitors or close homologues, although observed differential expression appeared to be biased towards unique transcripts. The use of 3′ capture enhanced the ability to unambiguously identify homologues within the B. napus transcriptome but was limited by tag length. The ability to comprehensively catalogue gene expression in polyploid species could be transformed by the application of cost-efficient next generation sequencing technologies that will capture millions of long sequence tags.

scholarly journals Mutanome Engineered RNA Immunotherapy: Towards Patient-Centered Tumor Vaccination

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Mathias Vormehr ◽  
Barbara Schrörs ◽  
Sebastian Boegel ◽  
Martin Löwer ◽  
Özlem Türeci ◽  
...  
Keyword(s):  
Target Selection ◽  
Efficient Production ◽  
Patient Centered ◽  
Sequencing Technologies ◽  
Cost Efficient ◽  
Potent Drug ◽  
Personalized Cancer ◽  
The Cost ◽  
Synthetic Mrna ◽  
Selection Of

Advances in nucleic acid sequencing technologies have revolutionized the field of genomics, allowing the efficient targeting of mutated neoantigens for personalized cancer vaccination. Due to their absence during negative selection of T cells and their lack of expression in healthy tissue, tumor mutations are considered as optimal targets for cancer immunotherapy. Preclinical and early clinical data suggest that synthetic mRNA can serve as potent drug format allowing the cost efficient production of highly efficient vaccines in a timely manner. In this review, we describe a process, which integrates next generation sequencing based cancer mutanome mapping,in silicotarget selection and prioritization approaches, and mRNA vaccine manufacturing and delivery into a process we refer to as MERIT (mutanome engineered RNA immunotherapy).

scholarly journals Genome-wide identification and expression analysis of the GhIQD gene family in upland cotton (Gossypium hirsutum L.)

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Lingling DOU ◽  
Limin LV ◽  
Yangyang KANG ◽  
Ruijie TIAN ◽  
Deqing HUANG ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Family ◽  
Segmental Duplication ◽  
Gene Expression Pattern ◽  
Cell Development ◽  
Fiber Cell ◽  
Fiber Cells ◽  
Genome Wide ◽  
Duplication Events ◽  
Signaling Receptors

Abstract Background Calmodulin (CaM) is one of the most important Ca2+ signaling receptors because it regulates diverse physiological and biochemical reactions in plants. CaM functions by interacting with CaM-binding proteins (CaMBPs) to modulate Ca2+ signaling. IQ domain (IQD) proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites. Results In this study, we identified 102 GhIQD genes in the Gossypium hirsutum L. genome. The GhIQD gene family was classified into four clusters (I, II, III, and IV), and we then mapped the GhIQD genes to the G. hirsutum L. chromosomes. Moreover, we found that 100 of the 102 GhIQD genes resulted from segmental duplication events, indicating that segmental duplication is the main force driving GhIQD gene expansion. Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells, suggesting that GhIQD genes may contribute to fiber cell development in cotton. In addition, we found that 20 selected GhIQD genes were highly expressed in various tissues. Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes. Conclusions Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA. Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes, as well as clues to breed better cotton varieties in the future.

scholarly journals DNA Methylation and Intra-Clonal Heterogeneity: The Chronic Myeloid Leukemia Model

Cancers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 3587
Author(s):  
Benjamin Lebecque ◽  
Céline Bourgne ◽  
Véronique Vidal ◽  
Marc G. Berger
Keyword(s):  
Dna Methylation ◽  
Chronic Myeloid Leukemia ◽  
Fusion Protein ◽  
Myeloid Leukemia ◽  
Kinase Inhibitors ◽  
Single Gene ◽  
Clonal Heterogeneity ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
The Impact

Chronic Myeloid Leukemia (CML) is a model to investigate the impact of tumor intra-clonal heterogeneity in personalized medicine. Indeed, tyrosine kinase inhibitors (TKIs) target the BCR-ABL fusion protein, which is considered the major CML driver. TKI use has highlighted the existence of intra-clonal heterogeneity, as indicated by the persistence of a minority subclone for several years despite the presence of the target fusion protein in all cells. Epigenetic modifications could partly explain this heterogeneity. This review summarizes the results of DNA methylation studies in CML. Next-generation sequencing technologies allowed for moving from single-gene to genome-wide analyses showing that methylation abnormalities are much more widespread in CML cells. These data showed that global hypomethylation is associated with hypermethylation of specific sites already at diagnosis in the early phase of CML. The BCR-ABL-independence of some methylation profile alterations and the recent demonstration of the initial intra-clonal DNA methylation heterogeneity suggests that some DNA methylation alterations may be biomarkers of TKI sensitivity/resistance and of disease progression risk. These results also open perspectives for understanding the epigenetic/genetic background of CML predisposition and for developing new therapeutic strategies.

Rapid-cycling Brassica Species: Inbreeding and Selection of B. campestris for Anther Culture Ability

1990 ◽  
Vol 65 (5) ◽  
pp. 557-566 ◽  
Author(s):  
F. N. ASLAM ◽  
M. V. MACDONALD ◽  
P. LOUDON ◽  
D. S. INGRAM
Keyword(s):  
Anther Culture ◽  
Brassica Species ◽  
Rapid Cycling ◽  
Selection Of

Analysis of yield and oil from a series of canola breeding trials. Part II. Exploring variety by environment interaction using factor analysisThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 1002-1016 ◽  
Author(s):  
B.R. Cullis ◽  
A.B. Smith ◽  
C.P. Beeck ◽  
W.A. Cowling
Keyword(s):  
Pedigree Information ◽  
Environment Interaction ◽  
Correlation Matrices ◽  
New Approach ◽  
Genome Wide ◽  
Selection Indices ◽  
New Varieties ◽  
Oilseed Brassicas ◽  
Analytic Models ◽  
Selection Of

Exploring and exploiting variety by environment (V × E) interaction is one of the major challenges facing plant breeders. In paper I of this series, we presented an approach to modelling V × E interaction in the analysis of complex multi-environment trials using factor analytic models. In this paper, we develop a range of statistical tools which explore V × E interaction in this context. These tools include graphical displays such as heat-maps of genetic correlation matrices as well as so-called E-scaled uniplots that are a more informative alternative to the classical biplot for large plant breeding multi-environment trials. We also present a new approach to prediction for multi-environment trials that include pedigree information. This approach allows meaningful selection indices to be formed either for potential new varieties or potential parents.

scholarly journals Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haomiao Cheng ◽  
Zhanru Shao ◽  
Chang Lu ◽  
Delin Duan
Keyword(s):  
Abiotic Stresses ◽  
Chitinase Activity ◽  
Thalassiosira Pseudonana ◽  
Centric Diatom ◽  
Carbon And Nitrogen ◽  
Genome Wide ◽  
Duplication Events ◽  
The Many ◽  
Chitinase Genes ◽  
Insight Into

Abstract Background The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms. Results Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution. Conclusions Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.

scholarly journals A Robust Rerank Approach for Feature Selection and Its Application to Pooling-Based GWA Studies

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Jia-Rou Liu ◽  
Po-Hsiu Kuo ◽  
Hung Hung
Keyword(s):  
Characteristic Curve ◽  
Real Data ◽  
Tuning Parameter ◽  
Practical Implementation ◽  
Tuning Parameters ◽  
Genome Wide ◽  
Feature Based ◽  
The Difference ◽  
Gwa Studies ◽  
Selection Of

Large-p-small-ndatasets are commonly encountered in modern biomedical studies. To detect the difference between two groups, conventional methods would fail to apply due to the instability in estimating variances int-test and a high proportion of tied values in AUC (area under the receiver operating characteristic curve) estimates. The significance analysis of microarrays (SAM) may also not be satisfactory, since its performance is sensitive to the tuning parameter, and its selection is not straightforward. In this work, we propose a robust rerank approach to overcome the above-mentioned diffculties. In particular, we obtain a rank-based statistic for each feature based on the concept of “rank-over-variable.” Techniques of “random subset” and “rerank” are then iteratively applied to rank features, and the leading features will be selected for further studies. The proposed re-rank approach is especially applicable for large-p-small-ndatasets. Moreover, it is insensitive to the selection of tuning parameters, which is an appealing property for practical implementation. Simulation studies and real data analysis of pooling-based genome wide association (GWA) studies demonstrate the usefulness of our method.

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