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PubMed2006

Accounting for background nucleotide composition when measuring codon usage bias: brilliant idea, difficult in practice.

The effective number of codons used in a gene is a commonly used measure of codon usage. It varies between 20 and 61 (standard genetic code) and indicates to which degree the entire genetic code is used. It is a drawback of this method that it does not take background composition into account. This led Novembre to introduce a variant called Nc' (Novembre JA. 2002. Accounting for background nucleotide composition when measuring codon usage bias. Mol Biol Evol 19:1390-4). In this letter, its properties are under the loupe, with special emphasis on phenomena relating to codon homozygosity. A theoretical misunderstanding regarding this estimator is explained in detail, notably Nc varies between 0 and 61 instead of 20 and 61 (with the standard genetic code). Practical examples from the genome of Pseudomonas aeruginosa are given which demonstrate that the problem is not just theoretical.

Base Composition↗

PubMed2002

Identification of truncated form of mouse HAX-1s gene (HAX-1xs) and characterization of its expression in small intestine and thymus of mice after burn injury.

Burn injury often leads to distant organ injury such as acute respiratory distress syndrome. We hypothesize that the pathophysiologic changes in distant organs result from orchestrated regulation of multiple genes in response to bum injury. Differential display was performed to identify genes regulated in distant organs in response to burn injury. Initial characterization of differentially amplified products demonstrated that HAX-1s mRNA was regulated in several distant organs after 18% total body surface area (TBSA) full-thickness flame burn injury in mice. Further characterization of HAX-1s mRNA revealed a novel transcript variant, which is rapidly and transiently induced in multiple tissues of mice within 6 h after burn injury. This novel HAX-1s transcript variant, called HAX-1xs, has an internal deletion of 252 nucleotides and single point mutation, resulting in reading frame intact. Western blot and immunohistochemical analyses of multiple tissues of mice using rabbit antibody raised against a 15-mer synthetic peptide clearly revealed the presence of HAX-1xs protein in the duodenum, and suggested that expression of HAX-1xs and/or HAX-1s was tissue- and cell type-specific. The expression of HAX-1xs and/or HAX-1s was distinctively regulated in Paneth cells of the duodenum and macrophages of the thymus after burn injury. These findings suggest that HAX-1xs has a different biological activity from HAX-1s and participates in a cascade of immediate-early cellular events in response to burn injury.

Adaptor Proteins, Signal Transducing↗

PubMed2025

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories.

Tumor evolution is driven by various mutational processes, ranging from single-nucleotide variants (SNVs) to large structural variants (SVs) to dynamic shifts in DNA methylation. Current short-read sequencing methods struggle to accurately capture the full spectrum of these genomic and epigenomic alterations due to inherent technical limitations. To overcome that, here we introduce an approach for long-read sequencing of single-cell derived subclones, and use it to profile 23 subclones of a mouse melanoma cell line, characterized with distinct growth phenotypes and treatment responses. We develop a computational framework for harmonization and joint analysis of different variant types in the evolutionary context. Uniquely, our framework enables detection of recurrent amplifications of putative driver genes, generated by independent SVs across different lineages, suggesting parallel evolution. In addition, our approach revealed gradual and lineage-specific methylation changes associated with aggressive clonal phenotypes. We also show our set of phylogeny-constrained variant calls along with openly released sequencing data can be a valuable resource for the development of new computational methods.

Journal Article↗

PubMed2005

Anti-D immunization by DEL red blood cells.

BACKGROUND: No data are available on the immunogenicity of extremely weak D variants called DEL. Evaluation of alloanti-D formation in a D- female patient after transfusion of apparently D- blood from an Austrian donor led to discovery of a so far unknown DEL type. STUDY DESIGN AND METHODS: Standard blood group serologic methods were applied. Molecular typing, RHD sequencing, and D epitope mapping was performed and the absolute D antigen density determined. RESULTS: After transfusion of RBCs typed D- by routine serology, the recipient developed alloanti-D. Further evaluation with an indirect antiglobulin test confirmed donor RBCs to be D-. Molecular typing, however, demonstrated the presence of the RHD gene in one donor, and RHD sequencing revealed a deletion of four nucleotides in RHD intron 5 (RHD IVS5-38del4) as the only difference compared to the normal RHD gene. Adsorption-elution techniques demonstrated a DEL phenotype without apparent loss of D epitopes. CONCLUSION: This study documents the clinical significance of the DEL phenotype in blood units that was capable of inducing anti-D in a recipient. Qualitative data are provided on D epitope expression in DEL RBCs.

Alleles↗

PubMed2006

Hb Woodville, a rare alpha-globin variant, caused by codon 6 mutation of the alpha1 gene.

Since 1995, the national programme for the prevention and control of severe thalassaemia has been implemented in Thailand. This programme is composed of the population screening in pregnant women and couples by osmotic fragility, HbE screening and the confirmation test using haemoglobin analyses by electrophoresis or chromatography. Thereafter, several hitherto unidentified haemoglobins (Hbs) with structural defects are increasingly described and these variants are now easily studied using DNA technology. In this study, the authors describe the haematology and molecular analyses in a 28-yr-old healthy female who was identified as having an exceptionally 'high HbA2' from haemoglobin analysis. Subsequent analyses demonstrated that observed atypical 'HbA2' was, in fact, a rare innocuous alpha-globin variant, called Hb Woodville [alpha 2 6(A4); Asp --> Tyr]. For the first time, this abnormal Hb species is characterised at the molecular level.

Adolescent↗

PubMed2004

The mosquito ribonucleotide reductase R2 gene: ultraviolet light induces expression of a novel R2 variant with an internal amino acid deletion.

Abstract Using RT-PCR, we examined expression of the ribonucleotide reductase R2 subunit (RNR-R2) in Aedes albopictus mosquito cells after treatment with ultraviolet light (UV). In control cells, a predominant band at 1.2 kb corresponded to the full-length cDNA. A smaller 650 bp band was unique to UV-treated cells. Sequence analysis showed that the 650 bp band encoded a protein with an internal deletion of 179 amino acids, relative to Ae. albopictus RNR-R2. The N-terminal twenty amino acids were identical between AalRNR-R2 and AalDeltaR2; downstream of the deletion, the proteins differed at only four residues. In AalDeltaR2, the internal deletion spanned five residues critical to RNR-R2 enzymatic activity, including a key tyrosine residue that generates an essential free radical. The full-length 46 kDa and truncated 25 kDa RNR-R2 proteins were shown to be expressed on Western blots, and to differ in their subcellular localization. Similarly, expression of the two proteins was differentially regulated during the cell cycle, and expression of AalDeltaR2 predominated after UV treatment. AalDeltaR2 resembled a human RNR-R2 variant called p53R2, which was induced by agents that damage DNA. As was the case with p53R2 and its antisense RNA, levels of AalDeltaR2 were diminished after treatment of mosquito cells with RNAi corresponding to p53 from Drosophila melanogaster. Examination of the AalRNR-R2 homologue in the Anopheles gambiae genome suggested that AalDeltaR2 resulted from precise splicing between Exons 1, 4 and 5, eliminating Exons 2 and 3. The likelihood that AalDeltaR2 is a non-enzymatic, functional participant in DNA metabolism is suggested by enhancement of DNA repair in an in vitro system and by the presence of a similar gene (rnr4) in yeast.

Aedes↗

PubMed1990

Abnormal tryptic peptide from the spectrin alpha-chain resulting from alpha- or beta-chain mutations: two genetically distinct forms of the Sp alpha I/74 variant.

Limited tryptic digestion of native spectrin (Sp) has revealed several variants in hereditary pyropoikilocytosis (HPP) and in a subset of patients with hereditary elliptocytosis (HE). In most cases, tryptic peptide corresponding to the alpha I (N-terminal) 80 kD domain is wholly or partially replaced by smaller fragments. These variants are provisionally designated according to the molecular weight of the most prominent new peptide. Partial amino acid sequences of the abnormal peptides and DNA analysis of the alpha-spectrin gene have shown that most variants result from substitution or insertion of an amino acid in the alpha I-domain. However, similar investigations did not detect any such abnormality in the spectrin alpha I-domain of an HE black kindred with one of the spectrin variants called Sp alpha I/74. In this kindred, restriction fragment length polymorphism studies and transmission of the genetic polymorphism relative to the alpha II-domain excluded the involvement of the alpha-chain in the pathological process. To ascertain whether the abnormal alpha I 74 kD peptide might be caused by a beta-chain mutation, we reconstituted hybrid dimers combining normal and HE Sp-chains. The tryptic peptide patterns of spectrin hybrid dimers containing HE alpha-chain and control beta-chain showed a normal 80 kD tryptic product. In contrast, the hybrid dimer containing normal alpha-chain and HE beta-chain gave rise to increased 74 kD peptide at the expense of the 80 kD, demonstrating that the mutation in this family resides in the beta-chain. The same method was used to show that in two other unrelated white kindreds, the elevated 74 kD peptide arose from a Sp alpha-chain defect. Thus an alteration in tryptic susceptibility within the N-terminal domain of the spectrin alpha-chain can be directed by a mutation in the beta-chain. The hybridization technique affords a definitive means of distinguishing between alpha- and beta-chain mutants.

Amino Acid Sequence↗

PubMed2006

The 12-lead ECG in patients with Mahaim fibers.

The aim of this review article is to discuss the electrocardiographic presentation of the so called variants of pre-excitation ("Mahaim fibers") during sinus rhythm and tachycardia.

Diagnosis, Differential↗

PubMed1996

Diagnosis and treatment of a child with the syndrome of apparent mineralocorticoid excess type 1.

We report the case of a 16-month-old boy who presented with chronic vomiting, failure to thrive, arterial hypertension and medullary nephrocalcinosis. Laboratory results revealed hypokalaemia, metabolic alkalosis, increased urinary potassium excretion and a hyporeninaemic hypoaldosteronism. Chromatographic determination of urinary steroid metabolites showed an abnormal elevation of tetrahydrocortisol and allo-tetrahydrocortisol compared to tetrahydrocortisone; this pattern of urinary steroid excretion is essential for the diagnosis of the syndrome of apparent mineralocorticoid excess type 1 and believed to be a result of the underlying metabolic defect, a decreased activity of the 11 beta-hydroxysteroid dehydrogenase. A second variant, called syndrome of apparent mineralocorticoid excess type 2, has similar clinical features but lacks the typical urinary steroid profile. Therapy with spironolactone resulted in growth, weight gain and blood pressure control.

11-beta-Hydroxysteroid Dehydrogenases↗

PubMed2002

A new green fluorescent protein construct for localizing and quantifying peptide release.

Green fluorescent protein (GFP)-tagged secretory proteins recently have been used for studying packaging of peptides, secretory vesicle dynamics, and regulation of peptide release. In cells in which release occurs from sites with an abundance of vesicles, it is difficult to resolve the exact location of individual exocytotic events with standard wide-field epifluorescence microscopy. Furthermore, current GFP constructs are not well suited for real-time measurement of peptide release from large numbers of cells. Here, we describe a new pH-sensitive construct that is designed for localizing and quantifying release of neuropeptides and peptide hormones. Specifically, the yellow GFP variant called Topaz was fused to proAtrial natriuretic peptide (proANP, also called proAtrial natriuretic factor). The fluorescence of this fusion protein is low in normally acidic secretory vesicles but increases approximately 10-fold upon neutralization. Furthermore, it is released upon depolarization of PC12 cells. Finally, individual release events can be detected as brief localized flashes of fluorescence. ProANF-Tpz should prove useful for studying single release events by wide-field epifluorescence microscopy and for fluorometer-based real-time peptide release measurements from high numbers of cells.

Animals↗

PubMed2025

From aerial drone to quantitative trait locus: leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa.

In recent years, accurate and low-cost variant calling has enabled the genotyping of large diversity panels for genome-wide association studies. As a result, phenotyping rather than genotyping is now the rate-limiting step, especially in field experiments. This has created a strong need for high-throughput, accurate, and low-cost in-field phenotyping. Here, we present a genome-wide association study (GWAS) study on 194 field-grown accessions of lettuce (Lactuca sativa). These accessions were non-destructively phenotyped at two time points 15 days apart using a drone equipped with an RGB and multispectral (MSP) camera. Our high-throughput phenotyping approach integrates an RGB- and MSP camera to measure the color and height of lettuce in this large-scale field experiment. We used the mean and other summary statistics, such as median, quantiles, skewness, kurtosis, minimum, and maximum to quantify different aspects of color and height variation in lettuce from the drone images. Using these summary statistics as traits for GWAS, we confirm several previously described genetic associations, now under field conditions, and identify additional novel associations for color and height traits in lettuce.

Lactuca↗

PubMed2004

Characterization of a complement-binding protein, DRS, from strains of Streptococcus pyogenes containing the emm12 and emm55 genes.

An extracellular protein of Streptococcus pyogenes, streptococcal inhibitor of complement (SIC), and its variant, called DRS (distantly related to SIC), are expressed by some S. pyogenes strains. SIC from type 1 (M1) isolates of S. pyogenes interferes with complement-mediated cell lysis, reportedly via its interaction with complement proteins. In this study we demonstrate that S. pyogenes strains carrying emm12 and emm55 (the genes for the M12 and M55 proteins, respectively) express and secrete DRS. This protein, like SIC, binds to the C6 and C7 complement proteins, and competition enzyme-linked immunosorbent assay experiments demonstrate that DRS competes with SIC for C6 and C7 binding. Similarly, SIC competes with DRS for binding to the complement proteins. Despite this, the recombinant DRS preparation showed no significant effect on complement function, as determined by lysis of sensitized sheep erythrocytes. Furthermore, the presence of DRS is not inhibitory to SIC activity.

Amino Acid Sequence↗

PubMed2026

Longitudinal characterization of mixed-genotype SARS-CoV-2 infections in a military cohort reveals compartmentalized viral populations.

UNLABELLED: Mixed-genotype severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are a concern due to the potential generation of novel recombinants that give rise to new variants. To better understand intra-host viral dynamics, we analyzed specimens from 24 participants from the U.S. Military Health System's Epidemiology, Immunology, and Clinical Characteristics of Emerging Infectious Diseases with Pandemic Potential COVID-19 cohort with suspected mixed-genotype SARS-CoV-2 infections. From an initial 24 suspected cases, we confirmed 17 as genuine coinfections and graded them by evidence: 7 were "strong"; 4 were "moderate"; 6 were "weak"; and 7 were deemed unlikely to be true mixed-genotype infections. Access to swabs from multiple body sites across the course of infection allowed us to observe compartmentalization and shifts in variant dominance that would have been missed by a single-timepoint analysis, as well as one recombinant Omicron BA.1/BA.2 genome. By using an evidence-based bioinformatic framework to assess sequencing data from well-characterized clinical cases, we distinguished genuine coinfections from bioinformatic artifacts. Our findings emphasize the importance of both extensive specimen collection and careful bioinformatic approaches in ascertaining dual genotype infections. IMPORTANCE: Novel recombinants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) arise from coinfections with different lineages, but mixed infections are not screened for despite risk to public health, and most surveillance relies on single swabs. We analyzed a longitudinal data set with specimens from multiple body sites, providing an opportunity to assess intra-host dynamics. To distinguish true coinfection from bioinformatic artifacts with confidence, we applied a framework that grades evidence for mixed genotypes by incorporating lineage and clade with manually validated variant calls. This allowed investigation beyond abundance levels of mixed genotypes within a single specimen, including observations of compartmentalization and a recombinant virus. This work enables further study of evolutionary, immunological, and clinical implications of mixed SARS-CoV-2 genotypes. Detecting dual-genotype infections and discriminating between true dual-genotype infection vs potential bioinformatics-based artifacts support public health and military readiness. These efforts provide evidence to bolster decision-making in molecular epidemiological studies to track transmission and for the choice of effective countermeasures.

SARS-CoV-2↗

PubMed2000

Identification of rpaP1-5 and rpaP2-6 genes encoding two additional variants of the 60S acidic ribosomal proteins of Schizosaccharomyces pombe.

In the fission yeast, four genes (rpaP1-1, rpaP1-3, rpaP2-2, and rpaP2-4) encoding two variants of the RpaP1 and RpaP2 ribosomal proteins (rp) have been characterized. We have identified cDNA for additional variants called RpaP1.5 and RpaP2.6. Sequence comparison suggests that RpaP1.5 diverged before RpaP1.1 and RpaP1.3 and that RpaP2.6 is closer to RpaP2.2 than to RpaP2.4. The corresponding genes, rpaP1-5 and rpaP2-6, are transcribed coordinately with other rp genes.

Amino Acid Sequence↗

PubMed2002

Expression of the Na+-HCO-3 cotransporter NBC4 in rat kidney and characterization of a novel NBC4 variant.

The purpose of the present studies was to examine the renal distribution and functional properties of Na(+)-HCO(3)(-) cotransporter type 4 (NBC4), the latest NBC isoform to be identified. Zonal distribution studies in rat kidney by Northern blot hybridization and RT-PCR demonstrated that NBC4 is highly abundant in the outer medulla and cortex but is low in the inner medulla. Nephron segment distribution studies indicated that NBC4 is predominantly expressed in the medullary and cortical thick ascending limb of the loop of Henle. Using specific primers on the basis of the published sequence (GenBank accession no. AF-207661), a full-length NBC4 variant was cloned from human liver and examined. The sequence of this variant (called NBC4e) is shorter by 86 amino acids vs. the published sequence. Xenopus laevis oocytes injected with the full-length NBC4e cRNA were compared with NBC1-expressing oocytes. Although exposure of NBC1-expressing oocytes to CO(2)/HCO(3)(-) resulted in immediate hyperpolarization, the NBC4-expressing oocytes did not show any alteration in membrane potential. NBC activity in oocytes, assayed as the Na(+)-dependent, HCO(3)(-)-mediated intracellular pH recovery from acidosis, indicated that NBC4 is a DIDS-inhibitable NBC. We propose that NBC4 is expressed in the thick ascending limb of the loop of Henle and mediates cellular HCO(3)(-) uptake in this segment.

Animals↗

PubMed1998

Hereditary hypotrichosis simplex.

Hypotrichosis is a relatively common feature of a number of complex hereditary syndromes. However, the isolated variant, called hereditary hypotrichosis simplex (HHS), is especially uncommon. We present a Spanish family with 8 of 19 persons covering 4 generations affected by HHS. No associated ectodermal or other defects were noted. The pedigree was compatible with an autosomal dominant inheritance with variable penetrance.

Child↗

PubMed1978

Group-specific component, alpha1-antitrypsin and esterase D in Canadian Eskimos.

Three genetic markers - group-specific component (Gc), alpha1-antitrypsin, and esterase D - were examined in a population of Eskimos from Igloolik in the eastern Canadian Arctic. Gc and esterase D were found to be polymorphic. In addition to the common Gc types, an anodal variant called Gc Igloolik was found, probably identical to previously reported Gc Eskimo. Gene frequencies were Gc1: 0.6524, Gc2: 0.3373, GcIgl: 0.0104, for 338 Eskimos. Genetic types of alpha1-antitrypsin (Pi types) were mostly M, with two MS sibs who were half Caucasian, in 170 Eskimos. Frequencies of the esterase D allele in 336 Eskimos were EsD1: 0.7083, EsD2: 0.2917. The frequencies of Gc2 and EsD2 are both higher than are found in Caucasian populations.

Canada↗

PubMed2025

Reference genome bias in light of species-specific chromosomal reorganization and translocations.

BACKGROUND: Whole-genome sequencing efforts, have during the past decade, unveiled the central role of genomic rearrangements-such as chromosomal inversions-in evolutionary processes, including local adaptation in a wide range of taxa. However, employment of reference genomes from distantly or even closely related species for mapping and the subsequent variant calling can lead to errors and/or biases in the datasets generated for downstream analyses. RESULTS: Here, we capitalize on the recently generated chromosome-anchored genome assemblies for Arctic cod (Arctogadus glacialis), polar cod (Boreogadus saida), and Atlantic cod (Gadus morhua) to evaluate the extent and consequences of reference bias on population sequencing datasets (approx. 15-20 × coverage) for both Arctic cod and polar cod. Our findings demonstrate that the choice of reference genome impacts the mapping statistics, including mapping depth and mapping quality, as well as core population genetic estimates, such as heterozygosity levels, nucleotide diversity (π), and cross-species genetic divergence (DXY). Furthermore, using a more distantly related reference genome can lead to inaccurate detection and characterization of chromosomal inversions, i.e., in terms of size (length) and location (position), due to inter-chromosomal reorganizations between species. Additionally, we observe that some of the verified species-specific inversions are split across multiple genomic regions when mapped against a heterospecific reference. CONCLUSIONS: Inaccurate identification of chromosomal rearrangements as well as biased population genetic measures could potentially lead to erroneous interpretation of species-specific genomic diversity, impede the resolution of local adaptation, and thus, impact predictions of their genomic potential to respond to climatic and other environmental perturbations.

Animals↗