Glucocorticoid-induced lymphocytolysis: State of the genetic analysis

The glucocorticoid-induced lysis of lymphoid cell lines offers a genetic approach to steroid hormone action because unresponsive variants can easily be selected as resistant to this lytic effect. The present state of analysis of lymphocytolysis in two murine cell lines, the S49 T-lymphoma and the W7 thymoma, is reviewed. All glucocorticoid-resistant variants isolated so far result from various defects in the glucocorticoid receptor. The absence of variants blocked at another step of the lytic mechanism is discussed. The observed hemizygosity of the glucocorticoid receptor locus in the S49 line and the instability of cell hybrids illustrate some of the potential problems encountered in somatic cell genetics.     

Pre-selecting markers based on fixation index scores improved the power of genomic evaluations in a combined Yorkshire pig population

Combining different swine populations in genomic prediction can be an important tool, leading to an increased accuracy of genomic prediction using single nucleotide polymorphism (SNP) chip data compared with within-population genomic. However, the expected higher accuracy of multi-population genomic prediction has not been realized. This may be due to an inconsistent linkage disequilibrium (LD) between SNPs and quantitative trait loci (QTL) across populations, and the weak genetic relationships across populations. In this study, we determined the impact of different genomic relationship matrices, SNP density and pre-selected variants on prediction accuracy using a combined Yorkshire pig population. Our objective was to provide useful strategies for improving the accuracy of genomic prediction within a combined population. Results showed that the accuracy of genomic best linear unbiased prediction (GBLUP) using imputed whole-genome sequencing (WGS) data in the combined population was always higher than that within populations. Furthermore, the use of imputed WGS data always resulted in a higher accuracy of GBLUP than the use of 80K chip data for the combined population. Additionally, the accuracy of GBLUP with a non-linear genomic relationship matrix was markedly increased (0.87% to 15.17% for 80K chip data, and 0.43% to 4.01% for imputed WGS data) compared with that obtained with a linear genomic relationship matrix, except for the prediction of XD population in the combined population using imputed WGS data. More importantly, the application of pre-selected variants based on fixation index (Fst) scores improved the accuracy of multi-population genomic prediction, especially for 80K chip data. For BLUP|GA (BLUP approach given the genetic architecture), the use of a linear method with an appropriate weight to build a weight-relatedness matrix led to a higher prediction accuracy compared with the use of only pre-selected SNPs for genomic evaluations, especially for the total number of piglets born. However, for the non-linear method, BLUP|GA showed only a small increase or even a decrease in prediction accuracy compared with the use of only pre-selected SNPs. Overall, the best genomic evaluation strategy for reproduction-related traits for a combined population was found to be GBLUP performed with a non-linear genomic relationship matrix using variants pre-selected from the 80K chip data based on Fst scores.     

Mapping oxidations of apolipoprotein B-100 in human low-density lipoprotein by liquid chromatography-tandem mass spectrometry

Human low-density lipoprotein (LDL) is a major cholesterol carrier in blood. Elevated concentration of low-density lipoprotein, especially when oxidized, is a risk factor for atherosclerosis and other cardiac inflammatory diseases. Past research has connected free radical initiated oxidations of LDL with the formation of atherosclerotic lesions and plaque in the arterial wall. The role of LDL protein in the associated diseases is still poorly understood, partially due to a lack of structural information. In this study, LDL was oxidized by hydroxyl radical. The oxidized protein was then delipidated and subjected to trypsin digestion. Peptides derived from trypsin digestion were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Identification of modified peptide sequences was achieved by a database search against apo B-100 protein sequences using the SEQUEST algorithm. At different hydroxyl radical concentrations, oxidation products of tyrosine, tryptophan, phenylalanine, proline, and lysine were identified. Oxidized amino acid residues are likely located on the exterior of the LDL particle in contact with the aqueous environment or directly bound to the free radical permeable lipid layer. These modifications provided insight for understanding the native conformation of apo B-100 in LDL particles. The presence of some natural variants at the protein level was also confirmed in our study.     

Dynamin is primed at endocytic sites for ultrafast endocytosis

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Hormonal regulation of membrane phenotype

Incubation of rat hepatoma cells (HTC) in tissue culture with glucocorticoids alters several membrane properties characteristic of transformed cells, without affecting the growth rate of these cells. Variant cell lines resistant to dexamethasone inhibition of plasminogen activator production have been isolated using an agar-fibrin overlay technique to detect plasminogen activator production by individual colonies of HTC cells. The resistance to dexamethasone is not secondary to abnormal or absent glucocorticoid receptors, but due to a lesion in a later step in hormone action specific for plasminogen activator. These variants should prove useful for the study of the mechanism of steroid action as well as for the analysis of the role of proteases in the hormonal regulation of membrane function.     

The functional impact of BRCA1 BRCT domain variants using multiplexed DNA double-strand break repair assays

Pathogenic variants in BRCA1 are associated with a greatly increased risk of hereditary breast and ovarian cancer (HBOC). With the increased availability and affordability of genetic testing, many individuals have been identified with BRCA1 variants of uncertain significance (VUSs), which are individually detected in the population too infrequently to ascertain a clinical risk. Functional assays can be used to experimentally assess the effects of these variants. In this study, we used multiplexed DNA repair assays of variants in the BRCA1 carboxyl terminus to functionally characterize 2,271 variants for homology-directed repair function (HDR) and 1,427 variants for cisplatin resistance (CR). We found a high level of consistent results (Pearson’s r = 0.74) in the two multiplexed functional assays with non-functional variants located within regions of the BRCA1 protein necessary for its tumor suppression activity. In addition, functional categorizations of variants tested in the multiplex HDR and CR assays correlated with known clinical significance and with other functional assays for BRCA1 (Pearson’s r = 0.53 to 0.71). The results of the multiplex HDR and CR assays are useful resources for characterizing large numbers of BRCA1 VUSs.     

Potent cross-reactive antibodies following Omicron breakthrough in vaccinees

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SARS-CoV-2 Mutations and their Viral Variants

Mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occur spontaneously during replication. Thousands of mutations have accumulated and continue to since the emergence of the virus. As novel mutations continue appearing at the scene, naturally, new variants are increasingly observed.Since the first occurrence of the SARS-CoV-2 infection, a wide variety of drug compounds affecting the binding sites of the virus have begun to be studied. As the drug and vaccine trials are continuing, it is of utmost importance to take into consideration the SARS-CoV-2 mutations and their respective frequencies since these data could lead the way to multi-drug combinations. The lack of effective therapeutic and preventive strategies against human coronaviruses (hCoVs) necessitates research that is of interest to the clinical applications.The reason why the mutations in glycoprotein S lead to vaccine escape is related to the location of the mutation and the affinity of the protein. At the same time, it can be said that variations should occur in areas such as the receptor-binding domain (RBD), and vaccines and antiviral drugs should be formulated by targeting more than one viral protein.In this review, a literature survey in the scope of the increasing SARS-CoV-2 mutations and the viral variations is conducted. In the light of current knowledge, the various disguises of the mutant SARS-CoV-2 forms and their apparent differences from the original strain are examined as they could possibly aid in finding the most appropriate therapeutic approaches.