Mouse gene trap approach: identification of novel genes and characterization of their biological functions

1998 ◽  
Vol 76 (6) ◽  
pp. 1029-1037 ◽  
Author(s):  
Kenji Kitajima ◽  
Takashi Takeuchi
Keyword(s):  
Insertional Mutagenesis ◽  
Mouse Genome ◽  
Gene Trap ◽  
Mouse Gene ◽  
Selection Marker ◽  
Biological Functions ◽  
Exogenous Dna ◽  
Biological Phenomena ◽  
Endogenous Genes

The mouse gene trap strategy is an insertional mutagenesis involving an exogenous DNA, termed the trap vector, as a mutagen that produces a mutation in the mouse genome and a sequence tag to facilitate the isolation of the mutated genes. The trap vector consists of a reporter gene whose expression mimics that of the endogenous genes mutated and a selection marker that sorts cells bearing the inserted vector. Gene trap is a powerful method for identifying genes important in biological phenomena. Moreover, the method produces mutant organisms whose phenotypes provide invaluable information about the biological functions of the genes responsible for these phenotypes. Indeed, a number of genes essential for mouse embryogenesis have been identified by the gene trap method. Here, we describe the principle, results, and perspectives for applications of gene trap approach to the study of cell differentiation and lineage commitment.Key words: gene trap, embryogenesis, jumonji.

scholarly journals 4mCPred-CNN—Prediction of DNA N4-Methylcytosine in the Mouse Genome Using a Convolutional Neural Network

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 296
Author(s):  
Zeeshan Abbas ◽  
Hilal Tayara ◽  
Kil To Chong
Keyword(s):  
Mouse Genome ◽  
Matthews Correlation Coefficient ◽  
Biological Functions ◽  
Independent Dataset ◽  
Validation Test ◽  
Single Feature ◽  
Proposed Model ◽  
Dna Modifications ◽  
Feature Encoding ◽  
Feature Encoding Scheme

Among DNA modifications, N4-methylcytosine (4mC) is one of the most significant ones, and it is linked to the development of cell proliferation and gene expression. To know different its biological functions, the accurate detection of 4mC sites is required. Although we have several techniques for the prediction of 4mC sites in different genomes based on both machine learning (ML) and convolutional neural networks (CNNs), there is no CNN-based tool for the identification of 4mC sites in the mouse genome. In this article, a CNN-based model named 4mCPred-CNN was developed to classify 4mC locations in the mouse genome. Until now, we had only two ML-based models for this purpose; they utilized several feature encoding schemes, and thus still had a lot of space available to improve the prediction accuracy. Utilizing only a single feature encoding scheme—one-hot encoding—we outperformed both of the previous ML-based techniques. In a ten-fold validation test, the proposed model, 4mCPred-CNN, achieved an accuracy of 85.71% and Matthews correlation coefficient (MCC) of 0.717. On an independent dataset, the achieved accuracy was 87.50% with an MCC value of 0.750. The attained results exhibit that the proposed model can be of great use for researchers in the fields of biology and bioinformatics.

Fundamental relations and identities of fuzzy hyperalgebras

2021 ◽  
pp. 1-10
Author(s):  
Narjes Firouzkouhi ◽  
Abbas Amini ◽  
Chun Cheng ◽  
Mehdi Soleymani ◽  
Bijan Davvaz
Keyword(s):  
Universal Algebra ◽  
Equivalence Relation ◽  
Polynomial Function ◽  
Equivalence Relations ◽  
Fundamental Relation ◽  
Term Function ◽  
Biological Phenomena ◽  
Definition Of

Inspired by fuzzy hyperalgebras and fuzzy polynomial function (term function), some homomorphism properties of fundamental relation on fuzzy hyperalgebras are conveyed. The obtained relations of fuzzy hyperalgebra are utilized for certain applications, i.e., biological phenomena and genetics along with some elucidatory examples presenting various aspects of fuzzy hyperalgebras. Then, by considering the definition of identities (weak and strong) as a class of fuzzy polynomial function, the smallest equivalence relation (fundamental relation) is obtained which is an important tool for fuzzy hyperalgebraic systems. Through the characterization of these equivalence relations of a fuzzy hyperalgebra, we assign the smallest equivalence relation α i 1 i 2 ∗ on a fuzzy hyperalgebra via identities where the factor hyperalgebra is a universal algebra. We extend and improve the identities on fuzzy hyperalgebras and characterize the smallest equivalence relation α J ∗ on the set of strong identities.

Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor

2020 ◽  
Vol 22 (35) ◽  
pp. 19468-19479 ◽  
Author(s):  
Keiichiro Shiraga ◽  
Mako Urabe ◽  
Takeshi Matsui ◽  
Shojiro Kikuchi ◽  
Yuichi Ogawa
Keyword(s):  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Thermal Denaturation ◽  
Hydration Water ◽  
Biological Functions ◽  
Dielectric Sensor ◽  
Hydration State ◽  
Precise Characterization

The biological functions of proteins depend on harmonization with hydration water surrounding them.

High-throughput vectors for efficient gene silencing in plants

2002 ◽  
Vol 29 (10) ◽  
pp. 1217 ◽  
Author(s):  
Chris A. Helliwell ◽  
S. Varsha Wesley ◽  
Anna J. Wielopolska ◽  
Peter M. Waterhouse
Keyword(s):  
Gene Silencing ◽  
Insertional Mutagenesis ◽  
Single Step ◽  
Plant Genome ◽  
Specific Gene ◽  
Single Polymerase Chain Reaction ◽  
Efficient Gene ◽  
Gene Redundancy ◽  
Endogenous Genes ◽  
Rapid Generation

A major challenge in the post-genome era of plant biology is to determine the functions of all genes in the plant genome. A straightforward approach to this problem is to reduce or knockout expression of a gene with the hope of seeing a phenotype that is suggestive of its function. Insertional mutagenesis is a useful tool for this type of study but is limited by gene redundancy, lethal knockouts, non-tagged mutants, and the inability to target the inserted element to a specific gene. The efficacy of gene silencing in plants using inverted-repeat transgene constructs that encode a hairpin RNA (hpRNA) has been demonstrated by a number of groups, and has several advantages over insertional mutagenesis. In this paper we describe two improved pHellsgate vectors that facilitate rapid generation of hpRNA-encoding constructs. pHellsgate 4 allows the production of an hpRNA construct in a single step from a single polymerase chain reaction product, while pHellsgate 8 requires a two-step process via an intermediate vector. We show that these vectors are effective at silencing three endogenous genes in Arabidopsis, FLOWERING LOCUS C, PHYTOENE DESATURASE and ETHYLENE INSENSITIVE 2. We also show that a construct of sequences from two genes silences both genes.

scholarly journals Identification and characterization of a new isoform of small GTPase RhoE

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Yuan Dai ◽  
Weijia Luo ◽  
Xiaojing Yue ◽  
Wencai Ma ◽  
Jing Wang ◽  
...  
Keyword(s):  
Rho Gtpase ◽  
Small Gtpases ◽  
Small Gtpase ◽  
Biological Functions ◽  
Coding Region ◽  
Alternative Translation ◽  
Rho Family ◽  
Binding Capability ◽  
Identification And Characterization

Abstract The Rho family of GTPases consists of 20 members including RhoE. Here, we discover the existence of a short isoform of RhoE designated as RhoEα, the first Rho GTPase isoform generated from alternative translation. Translation of this new isoform is initiated from an alternative start site downstream of and in-frame with the coding region of the canonical RhoE. RhoEα exhibits a similar subcellular distribution while its protein stability is higher than RhoE. RhoEα contains binding capability to RhoE effectors ROCK1, p190RhoGAP and Syx. The distinct transcriptomes of cells with the expression of RhoE and RhoEα, respectively, are demonstrated. The data propose distinctive and overlapping biological functions of RhoEα compared to RhoE. In conclusion, this study reveals a new Rho GTPase isoform generated from alternative translation. The discovery provides a new scope of understanding the versatile functions of small GTPases and underlines the complexity and diverse roles of small GTPases.

scholarly journals Characterization of Poldip2 knockout mice: avoiding incorrect gene targeting

2021 ◽  
Author(s):  
Bernard Lassègue ◽  
Sandeep Kumar ◽  
Rohan Mandavilli ◽  
Keke Wang ◽  
Michelle Tsai ◽  
...  
Keyword(s):  
Knockout Mice ◽  
Cell Clone ◽  
Gene Trap ◽  
Rna Seq ◽  
Multifunctional Protein ◽  
Cellular Processes ◽  
Depth Study ◽  
Perinatal Lethality ◽  
Knockout Line

AbstractPOLDIP2 is a multifunctional protein whose roles are only partially understood. Our laboratory previously reported physiological studies performed using a mouse gene trap model, which suffered from two limitations: perinatal lethality in homozygotes and constitutive Poldip2 inactivation. To overcome these limitations, we developed a new conditional floxed Poldip2 model. The first part of the present study shows that our initial floxed mice were affected by an unexpected mutation, which was not readily detected by Southern blotting and traditional PCR. It consisted of a 305 kb duplication around Poldip2 with retention of the wild type allele and could be traced back to the original targeted ES cell clone. We offer simple suggestions to rapidly detect similar accidents, which may affect genome editing using both traditional and CRISPR-based methods. In the second part of the present study, correctly targeted floxed Poldip2 mice were generated and used to produce a new constitutive knockout line by crossing with a Cre deleter. In contrast to the gene trap model, many homozygous knockout mice were viable, in spite of having no POLDIP2 expression. To further characterize the effects of Poldip2 ablation in the vasculature, an RNA-seq experiment was performed in constitutive knockout carotid arteries. Results support the involvement of POLDIP2 in multiple cellular processes and provide new opportunities for future in-depth study of its functions.

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