Biomedical subjects

Daniel Nilsson

Publications and source records attributed to Daniel Nilsson.

15 recordsLinked to original sources

PubMed2026

Phenotypic and transcriptomic characterization of biallelic RNU2-2 developmental and epileptic encephalopathy.

OBJECTIVE: A significant proportion of individuals with suspected genetic developmental and epileptic encephalopathies (DEEs) remain unsolved following whole genome sequencing (WGS). Here we describe biallelic RNU2-2 variants causing a recently reported, severe, recessive DEE. METHODS: We screened individuals who have received WGS analyses at the Genomic Medicine Centre Karolinska for Rare Diseases for biallelic RNU2-2 variants. Deep phenotyping was performed through reviewing entire medical histories and phenotypic traits were transcribed to their corresponding Human Phenotype Ontology (HPO) term. HPO terms were used to generate pairwise phenotypic similarity scores and assess for significantly shared phenotype enrichment in the RNU2-2 sub-cohort. RNA sequencing analyses were performed in fibroblast and blood tissues to compare splicing events between RNU2-2 individuals and two independent control groups. RESULTS: We identified 14 individuals from nine families with 12 ultra-rare biallelic RNU2-2 variants clustering in the conserved 5' domains. Genotype data from 13 of 14 individuals has been reported previously as part of a larger cohort. All individuals presented with a highly concordant, severe DEE, characterized by severe to profound intellectual disability, inability to walk or communicate, hyperkinesia, and refractory seizures. Infantile spasms and tonic seizures were the predominant seizure types and a Lennox-Gastaut syndrome-like phenotype was common. These individuals had a significantly similar phenotypic signature when compared with 703 individuals with complex pediatric epilepsies (two-sided Monte Carlo permutation test, p = .005). RNA sequencing analyses showed aberrant splicing, with the most pronounced effects in fibroblast tissues in mutually exclusive exon and alternate 3' splice-site events, which were not detectable in blood. SIGNIFICANCE: We present deep phenotyping data and transcriptomic analyses that provide support for rare, 5' clustering biallelic RNU2-2 variants causing this novel, severe DEE. We propose an RNA sequencing methodology on fibroblast tissue for future validation of RNU2-2 variants.

autosomal recessive disease↗

PubMed2026

Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis.

MOTIVATION: Long-read sequencing (LRS) is increasingly used for human medical research and clinical diagnostics due to its capacity to generate complete genome information. However, there is a lack of robust and easy-to-use pipelines for comprehensive LRS data analysis. RESULTS: Here we present Nallo, a Nextflow pipeline for analysis of PacBio and Oxford Nanopore data, with additional support for rare disease research projects. The pipeline detects a wide range of genetic variants, performs genome assembly, and reports CpG methylation. It also enables annotation and ranking of variants based on their predicted functional consequences. AVAILABILITY AND IMPLEMENTATION: Nallo is available from GitHub: https://github.com/genomic-medicine-sweden/nallo.

Humans↗

PubMed2007

Charge recombination versus charge separation in donor-bridge-acceptor systems.

Optimizing the ratio of the rates for charge separation (CS) over charge recombination (CR) is crucial to create long-lived charge-separated states. Mastering the factors that govern the electron transfer (ET) rates is essential when trying to achieve molecular-scale electronics, artificial photosynthesis, and also for the further development of solar cells. Much work has been put into the question of how the donor-acceptor distances and donor-bridge energy gaps affect the electronic coupling, V(DA), and thus the rates of ET. We present here a unique comparison on how these factors differently influence the rates for CS and CR in a porphyrin-based donor-bridge-acceptor model system. Our system contains three series, each of which focuses on a separate charge-transfer rate-determining factor, the donor-acceptor distance, the donor-bridge energy gap, and last, the influence of the electron acceptor on the rate for charge transfer. In these three series both CS and CR are governed by superexchange interactions which make a CR/CS comparative study ideal. We show here that the exponential distance dependence increases slightly for CR compared to that for CS as a result of the increased tunneling barrier height for this reaction, in accordance with the McConnell superexchange model. We also show that the dependence on the tunneling barrier height is different for CS and CR. This difference is highly dependent on the electron acceptor and thus cannot solely be explained by the differences in the frontier orbitals of the electron donor in these porphyrin systems.

Journal Article↗

PubMed2006

A solanesyl-diphosphate synthase localizes in glycosomes of Trypanosoma cruzi.

We report the cloning of a Trypanosoma cruzi gene encoding a solanesyl-diphosphate synthase, TcSPPS. The amino acid sequence (molecular mass approximately 39 kDa) is homologous to polyprenyl-diphosphate synthases from different organisms, showing the seven conserved motifs and the typical hydrophobic profile. TcSPPS preferred geranylgeranyl diphosphate as the allylic substrate. The final product, as determined by TLC, had nine isoprene units. This suggests that the parasite synthesizes mainly ubiquinone-9 (UQ-9), as described for Trypanosoma brucei and Leishmania major. In fact, that was the length of the ubiquinone extracted from epimastigotes, as determined by high-performance liquid chromatography. Expression of TcSPPS was able to complement an Escherichia coli ispB mutant. A punctuated pattern in the cytoplasm of the parasite was detected by immunofluorescence analysis with a specific polyclonal antibody against TcSPPS. An overlapping fluorescence pattern was observed using an antibody directed against the glycosomal marker pyruvate phosphate dikinase, suggesting that this step of the isoprenoid biosynthetic pathway is located in the glycosomes. Co-localization in glycosomes was confirmed by immunogold electron microscopy and subcellular fractionation. Because UQ has a central role in energy production and in reoxidation of reduction equivalents, TcSPPS is promising as a new chemotherapeutic target.

Alkyl and Aryl Transferases↗

PubMed2006

Tumor of the conus medullaris treated with antituberculous therapy.

This case report concerns a 21-year-old man developing left leg paresis. Evaluation with magnetic resonance imaging (MRI) showed an intramedullary tumor in the conus region. He was planned for surgery but preoperative investigation indicated he had tuberculosis and the tumor was presumed to be a tuberculoma. Antituberculous therapy was started and the patient improved neurologically. The patient was followed clinically and with consecutive MRI during 2 years and the last MRI showed that the lesion had disappeared completely. Intramedullary tuberculomas are rare but important differential diagnosis in patients with spinal cord mass lesions. The role of medical and surgical treatment of intramedullary tuberculomas is discussed.

Antitubercular Agents↗

PubMed2006

Statistical theory of collisional energy transfer in molecular collisions. trans-stilbene deactivation by argon, carbon dioxide, and n-heptane.

Recent advances in experimental techniques have made it possible to measure the full conditional probability density P(E, E') of the energy transfer between two colliding molecules in the gas phase, one of which is highly energized and the other in thermal equilibrium at a given temperature. Data have now become available for trans-stilbene deactivation by the three bath gas molecules Ar, CO2, and n-heptane (C7H16). The initial energies of trans-stilbene are set to 10 000, 20 000, 30 000, and 40 000 cm (-1). The results show that exceptionally large amounts of energy are transferred in each collision. By application of our partially ergodic collision theory (PECT), we find that the energy transfer efficiency betaE ranges from a rather normal value of 0.15 for n-heptane at the highest excitation energy to 0.93-nearly in the ergodic collision limit-for the argon bath gas at high excitation energy. Generally, the PECT produces a good fit of the data except for the nearly elastic peak in the case of n-heptane, where PECT produces a rounded and downshifted peak in contrast to a sharply defined elastic maximum of the monoexponential functional fit produced from the original experimental data obtained by kinetically controlled selective ionization in the work of the group of Luther in Göttingen. This problem is analyzed and found to be related partly to the lack of treatment of glancing collisions in the theory with a remaining uncertainty due to the weak dependence of energy transfer efficiency on nearly elastic collisions. A summary of the present state of understanding shows that collisional activation and deactivation of reactant molecules is more efficient and more statistical than has been previously realized.

Journal Article↗

PubMed2005

Microfabricated solid-state dye lasers based on a photodefinable polymer.

We present a solid polymer dye laser based on a single-mode planar waveguide. The all-polymer device is self-contained in the photodefinable polymer SU-8 and may therefore easily be placed on any substrate and be integrated with polymer-based systems. We use as the active medium for the laser the commercially available laser dye Rhodamine 6G, which is incorporated into the SU-8 polymer matrix. The single-mode slab waveguide is formed by three-step spin-coating deposition: a buffer layer of undoped SU-8, a core layer of SU-8 doped with Rhodamine, and a cladding layer of undoped SU-8.

Journal Article↗

PubMed2005

Comparative genomics of trypanosomatid parasitic protozoa.

A comparison of gene content and genome architecture of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major, three related pathogens with different life cycles and disease pathology, revealed a conserved core proteome of about 6200 genes in large syntenic polycistronic gene clusters. Many species-specific genes, especially large surface antigen families, occur at nonsyntenic chromosome-internal and subtelomeric regions. Retroelements, structural RNAs, and gene family expansion are often associated with syntenic discontinuities that-along with gene divergence, acquisition and loss, and rearrangement within the syntenic regions-have shaped the genomes of each parasite. Contrary to recent reports, our analyses reveal no evidence that these species are descended from an ancestor that contained a photosynthetic endosymbiont.

Animals↗

PubMed2005

The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease.

Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.

Animals↗

PubMed2005

PECT model analysis and predictions of experimental collisional energy transfer probabilities P(E',E) and moments for azulene and biphenylene.

Experimental collisional energy transfer data from kinetically controlled selective ionization (KCSI) and ultraviolet absorption (UVA) experiments are analyzed in the framework of the partially ergodic collision theory (PECT). Collisions of azulene and biphenylene with different colliders are investigated as case studies. The downward wings of the P(E',E) energy transfer distributions obtained from the PECT model are fitted to the recently introduced "variable-shape"-exponential 3-parameter functional form of P(E',E) obtained from KCSI experiments, P(E',E) proportional, variant exp[-{(E - E')/(C(0) + C(1)E)}(Y)]. The PECT model is able to reproduce the characteristic dependence of the KCSI "shape parameter" Y on the choice of collider, the energy dependent width of the KCSI P(E',E) distributions, described by alpha(E) = C(0) + C(1)E, and the temperature dependence of the UVA data above room temperature. The statistical approach of PECT obviously captures the essence of large molecule energy transfer at chemically significant energies without the need of knowing specific features of the detailed collision dynamics. It therefore shows promise for predicting the shape of P(E',E) in master equation kernels for larger molecules.

Journal Article↗

PubMed2005

Strand asymmetry patterns in trypanosomatid parasites.

The genome organization of kinetoplastid parasites is unusual, with chromosomes containing several long regions of polycistronically transcribed genes. The regions where the direction of transcription switches have been hypothesized to contain origins of replication and possibly also centromers and promoters. We report that overall strand asymmetry patterns can be observed in Trypanosoma cruzi and Trypanosoma brucei with optima on strand-switch regions. The base skews of T. cruzi and T. brucei divergent strand-switches show patterns analogous to those for bacterial origins of replication, but they differ from those of Leishmania major. Bias in codon usage and the trypanosomatid unidirectional gene clusters predict most of this skew, but fail to properly explain the same trend in intergenic regions, as does the current knowledge of regulatory sequences.

Animals↗

PubMed2005

Messenger RNA processing sites in Trypanosoma brucei.

In Kinetoplastids, protein-coding genes are transcribed polycistronically by RNA polymerase II. Individual mature mRNAs are generated from polycistronic precursors by 5' trans splicing of a 39-nt capped leader RNA and 3' polyadenylation. It was previously known that trans splicing generally occurs at an AG dinucleotide downstream of a polypyrimidine tract, and that polyadenylation is coupled to downstream trans splicing. The few polyadenylation sites that had been examined were 100-400 nt upstream of the polypyrimidine tract which marked the adjacent trans splice site. We wished to define the sequence requirements for trypanosome mRNA processing more tightly and to generate a predictive algorithm. By scanning all available Trypanosoma brucei cDNAs for splicing and polyadenylation sites, we found that trans splicing generally occurs at the first AG following a polypyrimidine tract of 8-25 nt, giving rise to 5'-UTRs of a median length of 68 nt. We also found that in general, polyadenylation occurs at a position with one or more A residues located between 80 and 140 nt from the downstream polypyrimidine tract. These data were used to calibrate free parameters in a grammar model with distance constraints, enabling prediction of polyadenylation and trans splice sites for most protein-coding genes in the trypanosome genome. The data from the genome analysis and the program are available from: .

5' Untranslated Regions↗

PubMed2005

Adipocyte-specific overexpression of FOXC2 prevents diet-induced increases in intramuscular fatty acyl CoA and insulin resistance.

Insulin resistance plays a major role in the development of type 2 diabetes and may be causally associated with increased intracellular fat content. Transgenic mice with adipocyte-specific overexpression of FOXC2 (forkhead transcription factor) have been generated and shown to be protected against diet-induced obesity and glucose intolerance. To understand the underlying mechanism, we examined the effects of chronic high-fat feeding on tissue-specific insulin action and glucose metabolism in the FOXC2 transgenic (Tg) mice. Whole-body fat mass were significantly reduced in the FOXC2 Tg mice fed normal diet or high-fat diet compared with the wild-type mice. Diet-induced insulin resistance in skeletal muscle of the wild-type mice was associated with defects in insulin signaling and significant increases in intramuscular fatty acyl CoA levels. In contrast, FOXC2 Tg mice were completely protected from diet-induced insulin resistance and intramuscular accumulation of fatty acyl CoA. High-fat feeding also blunted insulin-mediated suppression of hepatic glucose production in the wild-type mice, whereas FOXC2 Tg mice were protected from diet-induced hepatic insulin resistance. These findings demonstrate an important role of adipocyte-expressed FOXC2 on whole-body glucose metabolism and further suggest FOXC2 as a novel therapeutic target for the treatment of insulin resistance and type 2 diabetes.

Acyl Coenzyme A↗

PubMed2004

A graphical tool for parasite genome annotation.

A graphical tool to facilitate rapid primary annotation of genomic sequence has been developed. Within a single interface the user can import sequences or database entries, run feature prediction programs and similarity searches, filter results, add additional manually found features and notes, and finally export annotations for database submission. Integrated rule-based feature corroboration and a novel decision support heuristic using ORF orientation, length and base-composition further enhances the efficiency of the annotation process without compromising flexibility. The program has been explicitly tailored to use in protozoan parasite genome projects, but can constitute a useful tool for prokaryote annotation as well. It is successfully being used by our lab in the Trypanosoma cruzi genome project, and can be obtained from the authors upon request.

Animals↗

PubMed2003

Selective charging of tRNA isoacceptors explains patterns of codon usage.

We modeled how the charged levels of different transfer RNAs (tRNAs) that carry the same amino acid (isoacceptors) respond when this amino acid becomes growth-limiting. The charged levels will approach zero for some isoacceptors (such as tRNA2Leu) and remain high for others (such as tRNA4Leu), as determined by the concentrations of isoacceptors and how often their codons occur in protein synthesis. The theory accounts for (synonymous) codons for the same amino acid that are used in ribosome-mediated transcriptional attenuation, the choices of synonymous codons in trans-translating transfermessenger RNA, and the overrepresentation of rare codons in messenger RNAs for amino acid biosynthetic enzymes.

Amino Acids↗