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At least 19 recordsLinked to original sources
PubMed2026

Optimization of functional genetics tools for a model tetraploid Capsella bursa-pastoris, with focus on homoeolog-aware gene editing.

Capsella bursa-pastoris is a recent allotetraploid and a promising model for studying early consequences of polyploidy. One of the intriguing questions in polyploid research is how new functions arise from initially identical or nearly identical homoeologous genes. Functional genetics tools, including genetic editing, can help to understand this process, but they have not been developed for C. bursa-pastoris yet. We present here the results of our study aimed at filling this gap. In particular, we compared the efficiency of floral dip transformation in six accessions of C. bursa-pastoris representing distant populations. The Asian clade accession PGL0025 had the highest efficiency of transformation (~ 1.1%). Comparison of Agrobacterium tumefaciens strains EHA105 and GV3101 (pMP90) showed that the latter is more effective. Also, we created a genome-wide gRNA database for all pairs of homoeologs of the PGL0001 accession of C. bursa-pastoris and integrated it into publicly available genome browser: https://t2e.online/igv_capsella_bursa-pastoris/ . We assessed the possibility of differential editing for two pairs of homoeologous genes with high sequence similarity (> 90%) both in vitro and in silico. Despite the test results that indicated off-target activity, we have succeeded in obtaining lines of plants with homozygous frameshift mutations in each of the homoeologs separately in vivo. We expect that these findings and resources will promote the use of C. bursa-pastoris as a model in functional genetics experiments, in particular, the studies of the fate of duplicated gene after polyploidization event.

Capsella↗
PubMedDate not supplied

Functional genetic damages and their possible role in the aging of eukaryote cells.

As a result of investigations of the functional acitivty of eukaryote cells damaged by ionizing radiation and alkylating mutagens under conditions of extreme loading, the authors have suggested that natural aging and aging accelerated by mutagens are based on a process of accumulation of functional genetic damages. The molecular nature of these damages differs from the mutational changes and repairable damages of DNA.

Aging↗
PubMed2025

Functional genetics of rice PISTILLATA genes reveals new roles and target genes in flowering time, female fertility, and parthenocarpy.

Floral organ identity is controlled largely by the combinatorial action of MADS domain homeotic transcription factors. Lodicules are specialized plant organs in cereals and grasses that are involved in floret opening and facilitate pollination and fertility in rice (Oryza sativa L.). To understand the mechanisms underlying the specification of the rice lodicule, we investigated the developmental functions of the rice PISTILLATA (PI) paralogs, OsMADS2, and OsMADS4. Null osmads2 mutants reiterated OsMADS2 nonredundant lodicule specification roles and revealed new roles in flowering time and floral organ number and fate. Doubly perturbed osmads2 osmads4kd florets had severe abnormalities, were female infertile, yet could initiate parthenocarpy. Ubiquitous OsMADS4 overexpression rescued osmads2 abnormalities. We also utilized genome-wide binding analyses and transcriptome profiling to identify putative target genes contributing to OsMADS2 functions. In osmads2d8/d8 null mutant, we observed deregulated genes in a plethora of processes including lodicule and stamen development, floral organ number, and cell wall development. Some examples are cell division regulators (Cyclin D6, Cyclin-P4-1-like), an aquaporin (PIP1A), a peptide transporter, a vascular developmental regulator (HOX1), and a cell wall modulator (GH9B16). The deregulation of these genes may be associated with the disrupted cell division, tissue differentiation, and physiology of the malformed lodicules in osmads2 and osmads2 osmads4kd florets. Altogether, we reveal novel roles for the rice PI paralogs in flowering time, panicle exsertion, and embryo sac differentiation, identify gene targets for lodicule development, and provide mechanistic insights on the functional diversification of rice PI paralogs.

Oryza↗
PubMed1976

Functional genetic expression of eukaryotic DNA in Escherichia coli.

We have isolated a segment of DNA from the eukaryote Saccharomyces cerevisiae (baker's yeast) as a viable molecular hybrid of bacteriophage lambda DNA which, when integrated into the chromosome of an E. coli histidine auxotroph, allows this bacterium to grow in the absence of histidine. The nonrevertable, histidine auxotroph lacks the enzymatic activity of imidazole glycerol phosphate (IGP) dehydratase (EC 4.2.1.19). From genetic experiments, we conclude that expression of the segment of yeast DNA results in the production of a diffusible substance and that transcription necessary for the complementation is most likely initiated from the segment of eukaryotic DNA.

Acetoxyacetylaminofluorene↗
PubMed2026

Whole-Genome Sequence Dataset of Rhodococcus qingshengii IEGM 267-Terpenoid Biotransformer Toward Genetic Functional Annotation.

Background/Objectives: Microbial biotransformation of monoterpenoids is a promising approach for obtaining bioactive compounds. Rhodococcus species are attractive biocatalysts due to their metabolic versatility and ability to transform hydrophobic substrates. In this study, we investigated the catalytic potential of Rhodococcus qingshengii IEGM 267 toward carveol isomers and explored genomic features that may underlie this activity. Methods: The strain was cultivated in mineral medium supplemented with (-)-trans-carveol. Biotransformation products were analyzed by TLC and GC-MS. The draft genome was sequenced, assembled, taxonomically assigned, and annotated using standard bioinformatics tools. Results: Rhodococcus qingshengii IEGM 267 efficiently converted (-)-trans-carveol to carvone. Genome analysis confirmed the taxonomic assignment of the strain and revealed a large repertoire of oxidoreductases, including monooxygenases, hydroxylases, and dehydrogenases. Seven genes encoding cytochrome P450-dependent oxygenases were identified as candidate enzymes potentially involved in carveol oxidation. Conclusions: R. qingshengii IEGM 267 is an efficient and stereoselective biocatalyst for (-)-trans-carveol oxidation. The results of bioinformatics analysis suggest an alternative enzymatic basis for this transformation and provide a foundation for future functional characterization.

Rhodococcus↗
PubMed2026

Zebrafish relatives as models for functional comparative genetics and genomics.

Closely related species, such as danionin fishes of the Danio, Danionella and Devario genera, often differ in their biology despite their shared evolutionary history, providing a platform for defining the molecular basis for the divergence of phenotypic traits. Such an approach requires the availability of large-scale genomic data, which have been provided by recent reports detailing the genomes of several danionins. Facilitated by the large number of genetic tools that are available for manipulation of the most studied member of this subgroup - the zebrafish, Danio rerio - the danionins have emerged as a useful comparative model system. Here we review their phylogeny and outline the phenotypic traits that are distinct to individual species or genera. We highlight how functional genetic tools such as interspecies hybridization, mutagenesis and transgenesis, as well as the recently reported genome assemblies, have enabled new avenues for hypothesis-driven and technology-driven exploration that collectively establish danionins as important genetic models for understanding a wide range of evolutionary innovations.

Journal Article↗
PubMed1977

Rh sytem. Genetics and function.

Little is known about the exact genetic control of the Rh system. The Rh antigen is a large protein molecule carrying many antigenic determinants. The structural genes controlling its production comprise a gene complex that has probably evolved by unequal crossover and mutation at the duplicated points. No convincing evidence for crossing-over within the gene complex has been found since the discovery of Rh. Studies of Rhnull families provide evidence for unlinked control genes that influence the ability of the structural Rh genes to function. It was hoped that the Rhnull bloods would provide information to establish the function of the Rh antigen, because the antigen appears to be necessary to maintain the integrity of the red cell membrane. However, the abnormalities of the Rhnull cells (increased Na+K+ pumps) have not been tied directly to their lack of Rh antigens.

Alleles↗
PubMed2025

Peripheral Macular Endothelial Dystrophy: Clinical, Histopathologic, Genetic and Functional Characterization.

OBJECTIVE: To report a CHST6-associated corneal endothelial dystrophy. DESIGN: Prospective observational case series. PARTICIPANTS: Thirty-five individuals from seven families, including 13 affected individuals exhibiting corneal epithelial and stromal edema, peripheral posterior corneal macular opacities, and endothelial guttae, as well as 22 unaffected family members. METHODS: Whole-exome sequencing was performed in 3 families and Sanger sequencing of CHST6 was performed in all individuals. Histological examination of Descemet membrane (DM) excised at the time of endothelial keratoplasty was performed for three probands. Serum keratan sulfate (KS) levels were measured in members of six families. Functional analysis of identified mutations was performed using CHST6 promoter containing CHST6 expression vector in human keratocytes (HK) and corneal endothelial cells (HCEnC). MAIN OUTCOME MEASURES: Clinical phenotype; genetic analysis; functional analysis of identified CHST6 mutations; serum KS levels; histologic examinations of DM. RESULTS: All affected individuals demonstrated peripheral macular opacities at the level of DM. Visually significant corneal edema in affected individuals was successfully managed by endothelial keratoplasty. Genetic analysis demonstrated a rare CHST6 promoter mutation (c.-690G>C) in the homozygous state in affected individuals from three families and in the compound heterozygous state with a CHST6 coding mutation (p.R211Q, p.Y268C or p.P280L) in affected individuals from the other four families. In silico analysis predicted c.-690G>C to be a regulatory variant, located at the RNA polymerase II binding site. Functional analysis in vitro demonstrated that c.-690G>C leads to increased KS sulfation in the corneal endothelium and DM, with no change of KS sulfation in keratocytes. Histologic examination of DM from affected individuals revealed elevated levels of sulfated and non-sulfated KS in DM and endothelium, consistent with the functional analysis. Minimum changes in serum sulfated KS levels were observed in affected individuals. CONCLUSIONS: We suggest the name Peripheral macular endothelial dystrophy (PMED) to describe this dystrophy that is characterized by peripheral posterior corneal macular opacities and endothelial dysfunction without stromal haze or opacities. Given that both PMED and macular corneal dystrophy are associated with promoter and coding region mutations in CHST6, we propose that they be categorized as CHST6-associated corneal dystrophies.

Humans↗
PubMed2026

[Genetic and functional characterization of a novel KIT splicing variant in a Chinese three-generation pedigree with piebaldism].

OBJECTIVES: To investigate the genetic etiology of a three-generation pedigree affected with piebaldism. METHODS: Next-generation sequencing and Sanger sequencing were employed to detect and verify gene variants. Bioinformatics tools were used to predict the effects of candidate variants on splicing and protein function. RT-PCR and Sanger sequencing were further performed to validate the impact of the variant on RNA splicing, and homology modeling was applied to predict its effect on the three-dimensional structure of the KIT protein. The pathogenicity of the variant was then classified according to the guidelines of the American College of Medical Genetics and Genomics (ACMG) and the UK Association for Clinical Genomic Science (ACGS). RESULTS: A heterozygous insertion variant near the splice site, c.1990+8_1990+9insTGCACCATTGGAGGTAAA, was identified in the KIT gene in the proband and was found to co-segregate with the phenotype within the family. RT-PCR and cDNA sequencing revealed that this variant led to aberrant splicing during transcription, resulting in a 21 bp in-frame insertion in the mRNA, which encodes an extra 7 amino acids within the tyrosine kinase domain and may thus affect protein function. In silico predictions, together with the experimental findings, supported classification of this variant as likely pathogenic according to relevant variant interpretation guidelines. CONCLUSIONS: The heterozygous splice-site insertion variant KIT:c.1990+8_1990+9insTGCACCATTGGAGGTAAA is the genetic cause of piebaldism in this pedigree.

Genetics diagnosis↗
PubMed2024

Obesity: exploring its connection to brain function through genetic and genomic perspectives.

Obesity represents an escalating global health burden with profound medical and economic impacts. The conventional perspective on obesity revolves around its classification as a "pure" metabolic disorder, marked by an imbalance between calorie consumption and energy expenditure. Present knowledge, however, recognizes the intricate interaction of rare or frequent genetic factors that favor the development of obesity, together with the emergence of neurodevelopmental and mental abnormalities, phenotypes that are modulated by environmental factors such as lifestyle. Thirty years of human genetic research has unveiled >20 genes, causing severe early-onset monogenic obesity and ~1000 loci associated with common polygenic obesity, most of those expressed in the brain, depicting obesity as a neurological and mental condition. Therefore, obesity's association with brain function should be better recognized. In this context, this review seeks to broaden the current perspective by elucidating the genetic determinants that contribute to both obesity and neurodevelopmental and mental dysfunctions. We conduct a detailed examination of recent genetic findings, correlating them with clinical and behavioral phenotypes associated with obesity. This includes how polygenic obesity, influenced by a myriad of genetic variants, impacts brain regions associated with addiction and reward, differentiating it from monogenic forms. The continuum between non-syndromic and syndromic monogenic obesity, with evidence from neurodevelopmental and cognitive assessments, is also addressed. Current therapeutic approaches that target these genetic mechanisms, yielding improved clinical outcomes and cognitive advantages, are discussed. To sum up, this review corroborates the genetic underpinnings of obesity, affirming its classification as a neurological disorder that may have broader implications for neurodevelopmental and mental conditions. It highlights the promising intersection of genetics, genomics, and neurobiology as a foundation for developing tailored medical approaches to treat obesity and its related neurological aspects.

Humans↗
PubMed1977

Functional and genetic analysis of Ia antigens.

Using negative selection with anti-Ia serum and complement, Ia-"negative" lymphocyte populations give rise to clonal progeny which produce only IgM antibody, whereas Ia-positive lymphocytes generate B-cell progeny which produce IgG or both IgM and IgG antibody. The responder cell in the mixed lymphocyte reaction and the precursor and effector cells in cell-mediated lympholysis appear to be Ia-"negative" lymphocyte subpopulations. Helper T cells in some system are Ia-positive, and allotype suppressor T cells are also Ia-positive. Allogenic effect factor produced in the usual manner functions as an antigen nonspecific helper factor for several different H-2 haplotypes. However, when allogenic effect factor is produced from a mixed lymphocyte culture between responder lymphocytes treated with anti-Ia and complement and irradiated stimulator lymphocytes treated with anti-Thy-1.2 and complement, this "restricted" AEF is sharply restricted in the haplotypes it can stimulate. "Restricted" AEF produced in this manner with B10.BR responder cells and B10.S stimulator cells helps B10.S T-cell-depleted, hap-ten-primed spleen B cells but does not help B10.BR spleen cells. This raises the possibility that the Ia antigens in AEF may be derived from the stimulator B cells and/or macrophages rather than from the responder T cells.

Animals↗
PubMed1978

Determinant selection and macrophage function in genetic control of the immune response.

The immune response to insulin, in both mouse and guinea pig, is under control of H-linked immune response genes. When immunized with either pork or beef insulin in CFA, both strain 2 and 13 guinea pigs respond by antigen-specific lymphocyte proliferation and synthesis of specific antibody. The specificities of the elicited antibodies and indistinguishable between these inbred strains. By constrast, strain 2 T cells recognized a distinct region of the A chain alpha loop consisting of amino acid residues 8, 9 and 10, while strain 13 T cells see an as yet undefined region of the B chain. H2b (A chain alpha loop responder) and H2d (B chain responder) mice similarly discriminate which areas of the molecule are recognized by their T lymphocytes. The function of the Ir gene in both the guinea pig and mouse appears to be an intramolecular selection of discrete regions within the antigen for recognition by the T cell. The data presented suggest that this function operates at the level of the macrophage.

Animals↗
PubMed2003

Genetics and functional genomics of type 2 diabetes mellitus.

Genome-wide studies of transcription in the skeletal muscle of type 2 diabetic patients have identified coordinated changes in the expression of genes involved in oxidative phosphorylation, and have underlined the central role of the oxidative-phosphorylation regulator, PCG1alpha. These findings help unravel the complex pathogenesis and inheritance of polygenic type 2 diabetes mellitus.

Animals↗
PubMed1979

[Hemoglobins, XXVIII. Phosphate-protein-interaction, gene expression and function: the genetic and allosteric control of the oxygen affinity of the fetal blood (author's transl)].

This work describes possible molecular mechanisms concerning the control of oxygen affinity in fetal blood of mammalia. There is a genetic control of oxygen affinity through a fetal gene: at constant phosphate concentration (Hb less than P2-glycerate) in humans there is a hemoglobin with only five binding sites to 2,3-bisphosphoglycerate, resulting in an increased oxygen affinity. In several species (sheep, cattle, goat) with Met-Leu as the N-terminal group of the beta-chains, the 2,3-bisphosphoglycerate binding sites are deleted in positions beta 1 and beta 2, so that the regulation is phosphate-independent and thus providing a fetal hemoglobin with an increased oxygen affinity. The allosteric control is observed in pigs. In the postembryonal development "adult" hemoglobin with seven contacts (beta-chains) is demonstrated. The increased oxygen affinity is achieved here by a reduced biosynthesis of 2,3-bisphosphoglycerate (Hb greater than P2-glycerate) (Rapoport-Luebering-cycle). The functional control is discussed with respect to the ontogeny of the hemoglobins.

Allosteric Regulation↗
PubMed1978

Genetic and functional characterization of an antiserum to the lipid A-specific triggering receptor on murine B lymphocytes.

The inheritance of responsiveness to lipopolysaccharide (LPS), and of a marker recognized in LPS-reactive cells by a heterologous antiserum, was studied in crosses between C3H/HeJ (nonresponder) and C3H/Tif (high responder) mice. F1 hybrid mice show codominant expression of these traits: (a) LPS-reactive cells are only hlaf as frequent in the hybrids as in the high responder parent; (b) the serologically defined marker is expressed in half as many cells in the hybrids as in the high responder parent. In backcross generations, both LPS responsiveness and this serological marker segregated into high, intermediate, and nonresponders. LPS or free lipid A, but not two other B cell mitogens (lipoprotein, and purified protein derivative of tuberculin), compete with the antiserum for binding to the B cell surface membrane, and are capable of completely inhibiting such binding without interfering with the binding of a-ti-Ig antibodies or complexes to Fc receptors. The addition of an IgG fraction of the antiserum to B cell cultures results in exponetial growth of the cells and in maturation to antibody secretion. This mitogenic activity is dose-depedent and absorbable on spleen cells from LPS high responder mice. Taken together, these observations suggest that this antiserum contains antibodies to the lipid A-specific triggering receptor on B lymphocytes.

Animals↗