Kabat's database has often been used to design mouse Vh gene-specific 5' primers. The emphasis was mostly on constructing a universal (degenerate) 5' primer or 5' primer set, which would be able to match every mouse Vh gene. We were interested in finding oligonucleotides that could be used as primers or probes that can discriminate between the different Vh gene families. To this end, Kabat's database was reordered into Vh gene families based on more than 80% homology to prototype Vh gene family sequences. Rules were formulated for adequate annealing of putative primers to their respective genes. Putative primers were derived from the consensus sequences of the Vh gene families. A computer program was designed to systematically screen for the most optimal 5' and 3' Vh gene family-specific primers. This program enabled us to find a set of framework I-specific 5' primers, as well as a set of framework III-specific 3' primers. The found primers were also tested for their use as Vh gene family-specific probes.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/s0022-1759(01)00396-9 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
An augmented transformer model trained on protein family specific variant data leads to improved prediction of variants of uncertain significance.
Hum Genet
January 2025
TCS Research, Tata Consultancy Services, Hyderabad, India.
Variants of uncertain significance (VUS) represent variants that lack sufficient evidence to be confidently associated with a disease, thus posing a challenge in the interpretation of genetic testing results. Here we report an improved method for predicting the VUS of Arylsulfatase A (ARSA) gene as part of the Critical Assessment of Genome Interpretation challenge (CAGI6). Our method uses a transfer learning approach that leverages a pre-trained protein language model to predict the impact of mutations on the activity of the ARSA enzyme, whose deficiency is known to cause a rare genetic disorder, metachromatic leukodystrophy.
View Article and Find Full Text PDFTandemly duplicated Rubisco activase genes of cereals show differential evolution and response to heat stress.
Plant Mol Biol
December 2024
Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
Heat stress affects various components of photosynthetic machinery of which Rubisco activation inhibition due to heat sensitive Rubisco activase (RCA) is the most prominent. Detailed comparison of RCA coding genes identified a tandem duplication event in the grass family lineage where the duplicated genes showed very different evolutionary pattern. One of the two genes showed high level of sequence conservation whereas the second copy, although present only 1.
View Article and Find Full Text PDFReenacting a mouse genetic evolutionary arms race in yeast reveals SLXL1/SLX compete with SLY1/2 for binding to Spindlins.
bioRxiv
October 2024
Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI.
The house mouse X and Y chromosomes have recently acquired high copy number, rapidly evolving gene families representing an evolutionary arms race. This arms race between proteins encoded by X-linked / and Y-linked gene families can distort male offspring sex ratio, but how these proteins compete remains unknown. Here, we report how / and encoded proteins compete in a protein family-specific and dose-dependent manner using yeast.
View Article and Find Full Text PDFThe homeodomain regulates stable DNA binding of prostate cancer target ONECUT2.
Nat Commun
October 2024
Department of Biomedical Sciences, Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
The CUT and homeodomain are ubiquitous DNA binding elements often tandemly arranged in multiple transcription factor families. However, how the CUT and homeodomain work concertedly to bind DNA remains unknown. Using ONECUT2, a driver and therapeutic target of advanced prostate cancer, we show that while the CUT initiates DNA binding, the homeodomain thermodynamically stabilizes the ONECUT2-DNA complex through allosteric modulation of CUT.
View Article and Find Full Text PDFA zebrafish gene with sequence similarities to human uromodulin and GP2 displays extensive evolutionary diversification among teleost and confers resistance to bacterial infection.
Heliyon
September 2024
Department of Physiology, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Japan.
Article Synopsis
- Scientists studied a gene in zebrafish that helped them understand changes in a body part called the neuromuscular junction, especially in mutant fish that couldn't move.
- They discovered this gene is similar to other genes found in humans that help fight off bacteria and is part of a larger group of related genes in zebrafish.
- The researchers found that this gene helps young zebrafish survive better against infections, especially when they live in clean environments without germs.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!