Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells

Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.

Development of a machine learning framework for radiation biomarker discovery and absorbed dose prediction

Background

Molecular radiation biomarkers are an emerging tool in radiation research with applications for cancer radiotherapy, radiation risk assessment, and even human space travel. However, biomarker screening in genome-wide expression datasets using conventional tools is time-consuming and underlies analyst (human) bias. Machine Learning (ML) methods can improve the sensitivity and specificity of biomarker identification, increase analytical speed, and avoid multicollinearity and human bias.

Aim

To develop a resource-efficient ML framework for radiation biomarker discovery using gene expression data from irradiated normal tissues. Further, to identify biomarker panels predicting radiation dose with tissue specificity.

Methods

A strategic search in the Gene Expression Omnibus database identified a transcriptomic dataset (GSE44762) for normal tissues radiation responses (murine kidney cortex and medulla) suited for biomarker discovery using an ML approach. The dataset was pre-processed in R and separated into train and test data subsets. High computational cost of Genetic Algorithm/k-Nearest Neighbor (GA/KNN) mandated optimization and 13 ML models were tested using the caret package in R. Biomarker performance was evaluated and visualized via Principal Component Analysis (PCA) and dose regression. The novelty of ML-identified biomarker panels was evaluated by literature search.

Results

Caret-based feature selection and ML methods vastly improved processing time over the GA approach. The KNN method yielded overall best performance values on train and test data and was implemented into the framework. The top-ranking genes were Cdkn1a, Gria3, Mdm2 and Plk2 in cortex, and Brf2, Ccng1, Cdkn1a, Ddit4l, and Gria3 in medulla. These candidates successfully categorized dose groups and tissues in PCA. Regression analysis showed that correlation between predicted and true dose was high with R² of 0.97 and 0.99 for cortex and medulla, respectively.

Conclusion

The caret framework is a powerful tool for radiation biomarker discovery optimizing performance with resource-efficiency for broad implementation in the field. The KNN-based approach identified Brf2, Ddit4l, and Gria3 mRNA as novel candidates that have been uncharacterized as radiation biomarkers to date. The biomarker panel showed good performance in dose and tissue separation and dose regression. Further training with larger cohorts is warranted to improve accuracy, especially for lower doses.

Brassica sprouts exposed to microplastics: Effects on phytochemical constituents

Microplastics (MPs) can affect plant biomass, tissue composition, and root traits. However, the effects of MPs on the synthesis of secondary metabolites and on the accumulation of bioactive compounds remain poorly studied. The objective of this work was to analyze accumulation of bioactive compounds in broccoli and radish sprouts grown hydroponically in a substrate containing seven different toxic amounts (from very low to extremely high) of low-density polyethylene (PE). Radish was more severely affected by microplastic pollution than broccoli. The effect on the phytochemical composition was statistically significant in both species compared to control. In this aspect, glucosinolate (GSL) content was negatively affected by MPs decreasing from 182 to 124 mg 100 g^-1 at medium doses of MPs in broccoli, whereas these compounds drastically decreased from 253 to 151 mg 100 g^-1 at the same doses in radish. Anthocyanin content significantly increased until medium doses of MPs ranging from 6.28 to 11.44 mg 100 g^-1 in broccoli whereas in radish was from 2.44 to approximately 4 mg 100 g^-1. In addition, other morphological and physiological parameter were considered. The analysis of malondialdehyde (MDA) showed significant effects on broccoli and radish in all the MP treatments. The results revealed that high loads of MPs in the substrate affect growth parameters, lipid peroxidation rate estimated by MDA, and phytochemicals of broccoli and radish sprouts, with differences in response to MPs pollution and intensity between species.

TC-hunter: identification of the insertion site of a transgenic gene within the host genome

Background

Transgenic animal models are crucial for the study of gene function and disease, and are widely utilized in basic biological research, agriculture and pharma industries. Since the current methods for generating transgenic animals result in the random integration of the transgene under study, the phenotype may be compromised due to disruption of known genes or regulatory regions. Unfortunately, most of the tools that predict transgene insertion sites from high-throughput data are not publicly available or not properly maintained.

Results

We implemented TC-hunter, Transgene-Construct hunter, an open tool that identifies transgene insertion sites and provides simple reports and visualization aids. It relies on common tools used in the analysis of high-throughput data and makes use of chimeric reads and discordant read pairs to identify and support the transgenic insertion site. To demonstrate its applicability, we applied TC-hunter to four transgenic mice samples harboring the human PPM1D gene, a model used in the study of malignant tumor development. We identified the transgenic insertion site in each sample and experimentally validated them with Touchdown-polymerase chain reaction followed by Sanger sequencing.

Conclusions

TC-hunter is an accessible bioinformatics tool that can automatically identify transgene insertion sites from DNA sequencing data with high sensitivity (98%) and precision (92.45%). TC-hunter is a valuable tool that can aid in evaluating any potential phenotypic complications due to the random integration of the transgene and can be accessed at https://github.com/bcfgothenburg/SSF.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08376-0.

PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data

BACKGROUND

Processed pseudogenes (PΨgs) are disabled gene copies that are transcribed and may affect expression of paralogous genes. Moreover, their insertion in the genome can disrupt the structure or the regulatory region of a gene, affecting its expression level. These events have been identified as occurring mutations during cancer development, thus being able to identify PΨgs and their location will improve their impact on diagnostic testing, not only in cancer but also in inherited disorders.

RESULTS

We have implemented PΨFinder (P-psy-finder), a tool that identifies PΨgs, annotates known ones and predicts their insertion site(s) in the genome. The tool screens alignment files and provides user-friendly summary reports and visualizations. To demonstrate its applicability, we scanned 218 DNA samples from patients screened for hereditary colorectal cancer. We detected 423 PΨgs distributed in 96% of the samples, comprising 7 different parent genes. Among these, we confirmed the well-known insertion site of the SMAD4-PΨg within the last intron of the SCAI gene in one sample. While for the ubiquitous CBX3-PΨg, present in 82.6% of the samples, we found it reversed inserted in the second intron of the C15ORF57 gene.

CONCLUSIONS

PΨFinder is a tool that can automatically identify novel PΨgs from DNA sequencing data and determine their location in the genome with high sensitivity (95.92%). It generates high quality figures and tables that facilitate the interpretation of the results and can guide the experimental validation. PΨFinder is a complementary analysis to any mutational screening in the identification of disease-causing mutations within cancer and other diseases.

The enigmatic RNase MRP of kinetoplastids

The ribonucleoprotein RNase MRP is responsible for the processing of ribosomal RNA precursors. It is found in virtually all eukaryotes that have been examined. In the Euglenozoa, including the genera Euglena, Diplonema and kinetoplastids, MRP RNA and protein subunits have so far escaped detection using bioinformatic methods. However, we now demonstrate that the RNA component is widespread among the Euglenozoa and that these RNAs have secondary structures that conform to the structure of all other phylogenetic groups. In Euglena, we identified the same set of P/MRP protein subunits as in many other protists. However, we failed to identify any of these proteins in the kinetoplastids. This finding poses interesting questions regarding the structure and function of RNase MRP in these species.

Comparison of online learning designs during the COVID-19 pandemic within bioinformatics courses in higher education

MOTIVATION

Due to the worldwide COVID-19 pandemic, new strategies had to be adopted to move from classroom-based education to online education, in a very short time. The lack of time to set up these strategies, hindered a proper design of online instructions and delivery of knowledge. Bioinformatics-related training and other onsite practical education, tend to rely on extensive practice, where students and instructors have a face-to-face interaction to improve the learning outcome. For these courses to maintain their high quality when adapted as online courses, different designs need to be tested and the students' perceptions need to be heard.

RESULTS

This study focuses on short bioinformatics-related courses for graduate students at the University of Gothenburg, Sweden, which were originally developed for onsite training. Once adapted as online courses, several modifications in their design were tested to obtain the best fitting learning strategy for the students. To improve the online learning experience, we propose a combination of: (i) short synchronized sessions, (ii) extended time for own and group practical work, (iii) recorded live lectures and (iv) increased opportunities for feedback in several formats.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

RNA Sequencing of Hepatobiliary Cancer Cell Lines: Data and Applications to Mutational and Transcriptomic Profiling

Cancer cell lines allow the identification of clinically relevant alterations and the prediction of drug response. However, sequencing data for hepatobiliary cancer cell lines in general, and particularly gallbladder cancer (GBC), are sparse. Here, we apply RNA sequencing to characterize 10 GBC, eight hepatocellular carcinoma, and five cholangiocarcinoma (CCA) cell lines. RNA extraction, quality control, library preparation, sequencing, and pre-processing of sequencing data were implemented using state-of-the-art techniques. Public data from the MSK-IMPACT database and a large cohort of Japanese biliary tract cancer patients were used to illustrate the usage of the released data. The total number of exonic mutations varied from 7207 for the cell line NOZ to 9760 for HuCCT1. Researchers planning experiments that require TP53 mutations could use the cell lines NOZ, OCUG-1, SNU308, or YoMi. Mz-Cha-1 showed mutations in ATM, SNU308 presented SMAD4 mutations, and the only investigated cell line that showed ARID1A mutations was GB-d1. SNU478 was the cell line with the global gene expression pattern most similar to GBC, intrahepatic CCA, and extrahepatic CCA. EGFR, KMT2D, and KMT2C generally presented a higher expression in the investigated cell lines than in Japanese primary GBC tumors. We provide the scientific community with detailed mutation and gene expression data, together with three showcase applications, with the aim of facilitating the design of future in vitro cell culture assays for research on hepatobiliary cancer.

Cardiomyopathy with lethal arrhythmias associated with inactivation of KLHL24

Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiovascular disorder, yet the genetic cause of up to 50% of cases remains unknown. Here, we show that mutations in KLHL24 cause HCM in humans. Using genome-wide linkage analysis and exome sequencing, we identified homozygous mutations in KLHL24 in two consanguineous families with HCM. Of the 11 young affected adults identified, 3 died suddenly and 1 had a cardiac transplant due to heart failure. KLHL24 is a member of the Kelch-like protein family, which acts as substrate-specific adaptors to Cullin E3 ubiquitin ligases. Endomyocardial and skeletal muscle biopsies from affected individuals of both families demonstrated characteristic alterations, including accumulation of desmin intermediate filaments. Knock-down of the zebrafish homologue klhl24a results in heart defects similar to that described for other HCM-linked genes providing additional support for KLHL24 as a HCM-associated gene. Our findings reveal a crucial role for KLHL24 in cardiac development and function.

Antibiotic-resistant Staphylococcus aureus strains of swine origin: molecular typing and susceptibility to oregano (Origanum vulgare L.) essential oil and maqui (Aristotelia chilensis (Molina) Stuntz) extract

AIM

The molecular typing and the susceptibility of Staphylococcus aureus strains of swine origin to antibiotics, oregano (Origanum vulgare L.) essential oil (EO) and Chilean blackberry maqui (Aristotelia chilensis (Molina) Stuntz) extract were determined.

METHODS AND RESULTS

Twenty S. aureus strains of swine origin were subjected to molecular typing, of which six strains were selected for antimicrobial susceptibility testing. The epsilon test (Etest) was used to determine the antibiotic susceptibility. The susceptibility to natural antimicrobials (NAs): oregano EO, maqui extract, thymol (Thy) and carvacrol (Carv), was carried out using the disk diffusion method. The S. aureus strains were genetically diverse. All strains were resistant to at least one class of antibiotic, and two strains were multidrug-resistant. The minimum inhibitory concentration of oregano EO, Thy and Carv was 0·01-0·04%. Maqui extract did not show antistaphylococcal activity.

CONCLUSIONS

Natural antimicrobials extracted from oregano have an inhibitory activity against S. aureus strains from swine origin, with no effect using maqui extract.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study provides information about the characteristics of S. aureus strains of swine origin, and about the potential use of NAs from oregano to enhance the control of antibiotic-resistant S. aureus strains in the pork supply chain.

Hypoxia-regulated gene expression explains differences between melanoma cell line-derived xenografts and patient-derived xenografts

Cell line-derived xenografts (CDXs) are an integral part of drug efficacy testing during development of new pharmaceuticals against cancer but their accuracy in predicting clinical responses in patients have been debated. Patient-derived xenografts (PDXs) are thought to be more useful for predictive biomarker identification for targeted therapies, including in metastatic melanoma, due to their similarities to human disease. Here, tumor biopsies from fifteen patients and ten widely-used melanoma cell lines were transplanted into immunocompromised mice to generate PDXs and CDXs, respectively. Gene expression profiles generated from the tumors of these PDXs and CDXs clustered into distinct groups, despite similar mutational signatures. Hypoxia-induced gene signatures and overexpression of the hypoxia-regulated miRNA hsa-miR-210 characterized CDXs. Inhibition of hsa-miR-210 with decoys had little phenotypic effect in vitro but reduced sensitivity to MEK1/2 inhibition in vivo, suggesting down-regulation of this miRNA could result in development of resistance to MEK inhibitors.

Abstract 642: Hypoxia-regulated gene expression explains differences between cell line-derived xenografts and patient-derived xenografts

Cell line-derived xenografts (CDXs) are an integral part of drug efficacy testing during development of new pharmaceuticals against cancer but their accuracy in predicting clinical responses in patients have been debated. Patient-derived xenografts (PDXs) are thought to be more useful for predictive biomarker identification for targeted therapies, including metastatic melanoma, due to their similarities to human disease. Here, tumor biopsies from patients and ten widely-used melanoma cell lines were transplanted into immunocompromised mice to generate PDXs and CDXs, respectively. Gene expression profiles generated from the tumors of these PDXs and CDXs clustered into distinct groups, despite similar mutational signatures. Hypoxia-induced gene signatures and overexpression of the hypoxia-regulated miRNA hsa-miR-210 characterized CDXs. Inhibition of hsa-miR-210 with decoys had little phenotypic effect in vitro but resulted in reduced sensitivity to MEK1/2 inhibition in vivo, suggesting down-regulation of this miRNA could result in development of resistance to MEK inhibitors.

Citation Format: Joydeep Bhadury, Berglind O. Einarsdottir, Agnieszka Podraza, Roger Olofsson Bagge, Ulrika Stierner, Lars Ny, Marcela Dávila López, Jonas A. Nilsson. Hypoxia-regulated gene expression explains differences between cell line-derived xenografts and patient-derived xenografts. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 642.

Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells--Evidence of unique microRNA cargos

Melanoma cells release different types of extracellular vesicles (EVs) into the extracellular milieu that are involved with communication and signaling in the tumor microenvironment. Subsets of EVs include exosomes, microvesicles, and apoptotic bodies that carry protein and genetic (RNA) cargos. To define the contribution of the RNA cargo of melanoma cell derived EVs we performed small RNA sequencing to identify different small RNAs in the EV subsets. Using validated centrifugation protocols, we separated these EV subsets released by the melanoma cell line MML-1, and performed RNA sequencing with the Ion Torrent platform. Various, but different, non-coding RNAs were detected in the EV subsets, including microRNA, mitochondrial associated tRNA, small nucleolar RNA, small nuclear RNA, Ro associated Y-RNA, vault RNA and Y-RNA. We identified in total 1041 miRNAs in cells and EV subsets. Hierarchical clustering showed enrichment of specific miRNAs in exosomes, including hsa-miR-214-3p, hsa-miR-199a-3p and hsa-miR-155-5p, all being associated with melanoma progression. Comparison of exosomal miRNAs with miRNAs in clinical melanoma samples indicate that multiple miRNAs in exosomes also are expressed specifically in melanoma tissues, but not in benign naevi. This study shows for the first time the presence of distinct small RNAs in subsets of EVs released by melanoma cells, with significant similarities to clinical melanoma tissue, and provides unique insights into the contribution of EV associated extracellular RNA in cancer.

Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element

The majority of mitochondrial DNA replication events are terminated prematurely. The nascent DNA remains stably associated with the template, forming a triple-stranded displacement loop (D-loop) structure. However, the function of the D-loop region of the mitochondrial genome remains poorly understood. Using a comparative genomics approach we here identify two closely related 15 nt sequence motifs of the D-loop, strongly conserved among vertebrates. One motif is at the D-loop 5'-end and is part of the conserved sequence block 1 (CSB1). The other motif, here denoted coreTAS, is at the D-loop 3'-end. Both these sequences may prevent transcription across the D-loop region, since light and heavy strand transcription is terminated at CSB1 and coreTAS, respectively. Interestingly, the replication of the nascent D-loop strand, occurring in a direction opposite to that of heavy strand transcription, is also terminated at coreTAS, suggesting that coreTAS is involved in termination of both transcription and replication. Finally, we demonstrate that the loading of the helicase TWINKLE at coreTAS is reversible, implying that this site is a crucial component of a switch between D-loop formation and full-length mitochondrial DNA replication.

Encapsulated Essential Oils as an Alternative to Insecticides in Funnel Traps

Pheromone-lured funnel traps are widely used for pest monitoring and mass trapping in agricultural fields and stores. DDVP vapona (dichlorvos), the insecticide of choice as a killing agent inside traps, has been banned, and research on new products is being pursued. Essential oils (EO) could be an alternative if properly formulated. To test their potential, beads of encapsulated coriander and basil EO were tested in funnel traps in stores of almonds and pet foods during 2 mo. The number of adult moth (Plodia interpunctella (Hübner) and Ephestia kuehniella Zeller) dead captures was similar with either coriander or basil EO beads and with vapona tablets while there were more insects alive in the control. These preliminary results indicate a good potential for the development of such natural products as an alternative to synthetic insecticides to include them inside funnel traps.

Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions

The development of novel therapies against melanoma would benefit from individualized tumor models to ensure the rapid and accurate identification of biomarkers of therapy response. Previous studies have suggested that patient-derived xenografts (PDXes) could be useful. However, the utility of PDXes in guiding real-time treatment decisions has only been reported in anecdotal forms. Here tumor biopsies from patients with stage III and IV metastatic malignant melanoma were transplanted into immunocompromised mice to generate PDXes. 23/26 melanoma biopsies generated serially transplantable PDX models, and their histology, mutation status and expression profile resembled their corresponding patient biopsy. The potential treatment for one patient was revealed by an in vitro drug screen and treating PDXes with the MEK inhibitor trametinib. In another patient, the BRAF mutation predicted the response of both the patient and its corresponding PDXes to MAPK-targeted therapy. Importantly, in this unselected group of patients, the time from biopsy for generation of PDXes until death was significantly longer than the time required to reach the treatment phase of the PDXes. Thus, it could be clinically meaningful to use this type of platform for melanoma patients as a pre-selection tool in clinical trials.

Polyglucosan body myopathy caused by defective ubiquitin ligase RBCK1

Glycogen storage diseases are important causes of myopathy and cardiomyopathy. We describe 10 patients from 8 families with childhood or juvenile onset of myopathy, 8 of whom also had rapidly progressive cardiomyopathy, requiring heart transplant in 4. The patients were homozygous or compound heterozygous for missense or truncating mutations in RBCK1, which encodes for a ubiquitin ligase, and had extensive polyglucosan accumulation in skeletal muscle and in the heart in cases of cardiomyopathy. We conclude that RBCK1 deficiency is a frequent cause of polyglucosan storage myopathy associated with progressive muscle weakness and cardiomyopathy.

MTERF1 binds mtDNA to prevent transcriptional interference at the light-strand promoter but is dispensable for rRNA gene transcription regulation

Mitochondrial transcription termination factor 1, MTERF1, has been reported to couple rRNA gene transcription initiation with termination and is therefore thought to be a key regulator of mammalian mitochondrial ribosome biogenesis. The prevailing model is based on a series of observations published over the last two decades, but no in vivo evidence exists to show that MTERF1 regulates transcription of the heavy-strand region of mtDNA containing the rRNA genes. Here, we demonstrate that knockout of Mterf1 in mice has no effect on mitochondrial rRNA levels or mitochondrial translation. Instead, loss of Mterf1 influences transcription initiation at the light-strand promoter, resulting in a decrease of de novo transcription manifested as reduced 7S RNA levels. Based on these observations, we suggest that MTERF1 does not regulate heavy-strand transcription, but rather acts to block transcription on the opposite strand of mtDNA to prevent transcription interference at the light-strand promoter.

Effect of laser remelting on the tribological performance of thermal barrier coatings

Gas turbine's efficiency improves as operating temperature is increased. For this reason, metallic components used in turbine engines, for propulsion and power generation, are protected by thermal barrier coatings (TBC). Laser glazing has been used to enhance the oxidation and corrosion resistance of thermally sprayed TBC, but there is no information about the effect of this treatment on the tribological performance. ZrO2(CaO) top coat and NiAIMo bond coating were flame sprayed onto an AlSI 1045 carbon steel. The top coat was laser remelted and a densified ceramic layer was induced in the top surface of the ceramic coating. Both, the as sprayed and the laser remelted top coatings, were formed by cubic ZrO2 with some tetragonal precipitates. The grain size was reduced by the laser treatment. The mechanical properties and the local wear rate were evaluated by depth sensing indentation and scratch tests respectively. The nanoscale wear behaviour was always improved by the laser treatment.

Histone modifications influence mediator interactions with chromatin

The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator-histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization.

eGOB: eukaryotic Gene Order Browser

A large number of genomes have been sequenced, allowing a range of comparative studies. Here, we present the eukaryotic Gene Order Browser with information on the order of protein and non-coding RNA (ncRNA) genes of 74 different eukaryotic species. The browser is able to display a gene of interest together with its genomic context in all species where that gene is present. Thereby, questions related to the evolution of gene organization and non-random gene order may be examined. The browser also provides access to data collected on pairs of adjacent genes that are evolutionarily conserved.

AVAILABILITY

eGOB as well as underlying data are freely available at http://egob.biomedicine.gu.se

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

CONTACT

tore.samuelsson@medkem.gu.se.

Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes

The order of genes in eukaryotes is not entirely random. Studies of gene order conservation are important to understand genome evolution and to reveal mechanisms why certain neighboring genes are more difficult to separate during evolution. Here, genome-wide gene order information was compiled for 64 species, representing a wide variety of eukaryotic phyla. This information is presented in a browser where gene order may be displayed and compared between species. Factors related to non-random gene order in eukaryotes were examined by considering pairs of neighboring genes. The evolutionary conservation of gene pairs was studied with respect to relative transcriptional direction, intergenic distance and functional relationship as inferred by gene ontology. The results show that among gene pairs that are conserved the divergently and co-directionally transcribed genes are much more common than those that are convergently transcribed. Furthermore, highly conserved pairs, in particular those of fungi, are characterized by a short intergenic distance. Finally, gene pairs of metazoa and fungi that are evolutionary conserved and that are divergently transcribed are much more likely to be related by function as compared to poorly conserved gene pairs. One example is the ribosomal protein gene pair L13/S16, which is unusual as it occurs both in fungi and alveolates. A specific functional relationship between these two proteins is also suggested by the fact that they are part of the same operon in both eubacteria and archaea. In conclusion, factors associated with non-random gene order in eukaryotes include relative gene orientation, intergenic distance and functional relationships. It seems likely that certain pairs of genes are conserved because the genes involved have a transcriptional and/or functional relationship. The results also indicate that studies of gene order conservation aid in identifying genes that are related in terms of transcriptional control.

First report of a medullar cord compression secondary to osseous plasmacytoma successfully treated with bortezomib and dexamethasone

Medullar cord compression secondary to osseous plasmacytomas affecting the vertebrae is an oncological emergency. A 75-year-old woman with recurrent osseous plasmacytomas and thoracic spinal cord compression, previously treated with radiotherapy, was successfully treated with bortezomib and dexamethasone. Three years later, when the plasmacytoma and spinal cord compression relapsed, she was retreated with the same therapeutic scheme, achieving a new complete clinical remission. This is the first reported case of an excellent response to the combination of bortezomib and dexamethasone for spinal cord compression due to osseous plasmacytoma.

Conserved and variable domains of RNase MRP RNA

Ribonuclease MRP is a eukaryotic ribonucleoprotein complex consisting of one RNA molecule and 7-10 protein subunits. One important function of MRP is to catalyze an endonucleolytic cleavage during processing of rRNA precursors. RNase MRP is evolutionary related to RNase P which is critical for tRNA processing. A large number of MRP RNA sequences that now are available have been used to identify conserved primary and secondary structure features of the molecule. MRP RNA has structural features in common with P RNA such as a conserved catalytic core, but it also has unique features and is characterized by a domain highly variable between species. Information regarding primary and secondary structure features is of interest not only in basic studies of the function of MRP RNA, but also because mutations in the RNA give rise to human genetic diseases such as cartilage-hair hypoplasia.

Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components

The RNA molecules of the spliceosome are critical for specificity and catalysis during splicing of eukaryotic pre-mRNA. In order to examine the evolution and phylogenetic distribution of these RNAs, we analyzed 149 eukaryotic genomes representing a broad range of phylogenetic groups. RNAs were predicted using high-sensitivity local alignment methods and profile HMMs in combination with covariance models. The results provide the most comprehensive view so far of the phylogenetic distribution of spliceosomal RNAs. RNAs were predicted in many phylogenetic groups where these RNA were not previously reported. Examples are RNAs of the major (U2-type) spliceosome in all fungal lineages, in lower metazoa and many protozoa. We also identified the minor (U12-type) spliceosomal U11 and U6atac RNAs in Acanthamoeba castellanii, where U12 spliceosomal RNA as well as minor introns were reported recently. In addition, minor-spliceosome-specific RNAs were identified in a number of phylogenetic groups where previously such RNAs were not observed, including the nematode Trichinella spiralis, the slime mold Physarum polycephalum and the fungal lineages Zygomycota and Chytridiomycota. The detailed map of the distribution of the U12-type RNA genes supports an early origin of the minor spliceosome and points to a number of occasions during evolution where it was lost.

Early evolution of histone mRNA 3' end processing

The replication-dependent histone mRNAs in metazoa are not polyadenylated, in contrast to the bulk of mRNA. Instead, they contain an RNA stem-loop (SL) structure close to the 3' end of the mature RNA, and this 3' end is generated by cleavage using a machinery involving the U7 snRNP and protein factors such as the stem-loop binding protein (SLBP). This machinery of 3' end processing is related to that of polyadenylation as protein components are shared between the systems. It is commonly believed that histone 3' end processing is restricted to metazoa and green algae. In contrast, polyadenylation is ubiquitous in Eukarya. However, using computational approaches, we have now identified components of histone 3' end processing in a number of protozoa. Thus, the histone mRNA stem-loop structure as well as the SLBP protein are present in many different protozoa, including Dictyostelium, alveolates, Trypanosoma, and Trichomonas. These results show that the histone 3' end processing machinery is more ancient than previously anticipated and can be traced to the root of the eukaryotic phylogenetic tree. We also identified histone mRNAs from both metazoa and protozoa that are polyadenylated but also contain the signals characteristic of histone 3' end processing. These results provide further evidence that some histone genes are regulated at the level of 3' end processing to produce either polyadenylated RNAs or RNAs with the 3' end characteristic of replication-dependent histone mRNAs.

Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes

The RNases P and MRP are involved in tRNA and rRNA processing, respectively. Both enzymes in eukaryotes are composed of an RNA molecule and 9–12 protein subunits. Most of the protein subunits are shared between RNases P and MRP. We have here performed a computational analysis of the protein subunits in a broad range of eukaryotic organisms using profile-based searches and phylogenetic methods. A number of novel homologues were identified, giving rise to a more complete inventory of RNase P/MRP proteins. We present evidence of a relationship between fungal Pop8 and the protein subunit families Rpp14/Pop5 as well as between fungal Pop6 and metazoan Rpp25. These relationships further emphasize a structural and functional similarity between the yeast and human P/MRP complexes. We have also identified novel P and MRP RNAs and analysis of all available sequences revealed a K-turn motif in a large number of these RNAs. We suggest that this motif is a binding site for the Pop3/Rpp38 proteins and we discuss other structural features of the RNA subunit and possible relationships to the protein subunit repertoire.

[Reticulocyte response after immediate withdrawal of recombinant human erythropoietin in chronic hemodialysis patients]

The sudden interruption of recombinant human erythropoietin (rHuEPO) in end-stage renal disease (ESRD) patients leads to rapid anemization. The mechanisms of this phenomenon are, however, insufficiently understood. The present study examined the response to immediate rHuEPO withdrawal in dialysis patients.

METHODS

10 chronic hemodialysis (HD) patients regularly receiving rHuEPO were studied. rHuEPO was stopped and reinitiated after 7 days. Reticulocyte profile, haemoglobin and haematocrit were measured at 0, 7 and 15 days. As a complementary study, and with the purpose of analyzying whether uremia was a relevant factor, 10 non-uremic male Wistar rats were treated with rHuEPO. After two weeks, rHuEPO was withdrawn in 5 animals, and continued for 7 additional days in the remainder. The same variables than in the human study were determined.

RESULTS

Changes in reticulocyte subtypes from baseline to day 7 were: total 18.2 +/- 0.9 vs 14.3 +/- 1.8% (p < 0.06); high-fluorescence (HFR): 2.6 +/- 0.4 vs 0.75 +/- 0.2 (p < 0.001); medium-fluorescence (MFR): 13.0 +/- 1.1 vs 6.6 +/- 0.9% (p < 0.02); and low-fluorescence (LFR): 84.2 +/- 1.4 vs 92.7 +/- 1% (p NS). The baseline pattern was recovered upon 7 days of rHuEPO reinitiation (p NS). Mean hemoglobin and hematocrit decreased by day 14 (p < 0.02) in spite of rHuEPO reinitiation at day 7. In non-uremic rats, changes were similar to that in the ESRD patients.

CONCLUSION

rHuEPO induces changes in the reticulocyte pattern, consisting in a reduction of immature reticulocytes. These changes appear to be independent of the presence of uremia. Accordingly, complete rHuEPO withdrawal in HD patients will cause a rapidly-developing anaemia due to an alteration in the reticulocyte maturation series; therefore, sudden rHuEPO interruption should be avoided whenever is possible. As a collateral application, the specific changes described herein have potential use for detecting illegal administration of rHuEPO.

[Can we increase phosphate removal with conventional hemodialysis?]

BACKGROUND

The aim of the present study was to investigate the effect of different dialysate buffer and glucose concentrations, membrane surface (S) bigger than 2 m2 and increased dialysate flow (Qd) in phosphate (P) removal.

METHODS

A. First phase (5 patients): the following variations in dialysate composition were introduced. A: glucose 1.60 g/L, bicarbonate: 39 mEq/L, acetate 4 mEq/L, B: glucose 1.5 g/L bicarbonate 17 mEq/L, acetate 10 mEq/L; C: glucose 0, bicarbonate: 39 mEq/L, acetate 4 mEq/L; and D: glucose 0, bicarbonate 17 mEq/L, acetate 10 mEq/L. B. Second phase (14 patients): variations in S and Qd were: 1. Qd: 500 mL/min + Hemophan 2 m2, 2. Qd: 500 mL/min + Hemophan 2.6 m2, 3. Qd: 750 mL/min + Hemophan 2 m2, 4. Qd: 750 mL/min + Hemophan 2.6 m2.

RESULTS

Comparing HDs performed with low bicarbonate (B and D) respect to current buffer formulations (A and C), total P removal was 997.3 (+/- 237.3) vs 882 (+/- 216.1) mg (p NS). No differences were found by grouping the sessions according to glucose concentration. There were no significant differences in total phosphate removal between the two different S or Qd. The most important predictive factor of total P removal was the initial P and 2 hours serum P concentration, and PTH concentration.

CONCLUSIONS

i) Removal of P is better predicted by pre-dialysis P serum concentration; ii) P removal was not affected by the changes in bicarbonate and glucose concentration in the dialysate; iii) the increase of the dialyzer area between 2 and 2.6 m2 augments Kt/V, but without influencing P elimination; iv) a higher Qd does not determine significant differences in P removal and v) higher PTH is associated with a higher P elimination.

Impairment of renal vasodilation with l-arginine is related to more severe disease in untreated hypertensive patients

Data remain insufficient to place the decreased response to L-arginine in hypertensive patients within a consistent pathophysiological sequence. The aim of the present study in patients with essential hypertension was to assess the relationships between the response to L-arginine and a set of relevant clinical and laboratory parameters. In this prospective, interventional study, we administered L-arginine to untreated hypertensive individuals and healthy control subjects and measured the clearance of inulin and of para-aminohippurate and a set of biochemical and clinical variables. L-Arginine infusion revealed major differences between control subjects and 1 subgroup (group B) of hypertensive individuals. Group B hypertensives (n=18) had no increase in inulin clearance and no decrease in renal vascular resistance with L-arginine; however, in another subset of hypertensive patients (group A, n=27), the insulin clearance increased and renal vascular resistance decreased similar to the control group (group C, n=11). The ambulatory blood pressure monitoring in group B showed both an increased mean diastolic pressure and a "nondipper" pattern in the nocturnal regulation of arterial pressure. These findings in group B were accompanied by significant alterations in optic fundus and left ventricle hypertrophy and increased microalbuminuria (all, P<0.05). Furthermore, group B individuals had significantly lower values of HDL cholesterol and a higher baseline atherogenic index, plasma insulin level, and glucose/insulin index. We disclose a previously undescribed relationship between end organ repercussion and decreased renal hemodynamic response to L-arginine. Our results may help to understand the mechanisms that lead to target organ damage in hypertension.

N-(6-Amino-3,4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl) derivatives of glycine, valine, serine, threonine and methionine: interplay of molecular, molecular-electronic and supramolecular structures

In each of N-(6-amino-3, 4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)valine, C(10)H(15)N(5)O(4) (3) (orthorhombic, P2(1)2(1)2(1)), N-(6-amino-3, 4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)serine monohydrate, C(8)H(11)N(5)O(5).H(2)O (4) (orthorhombic, P2(1)2(1)2(1)), and N-(6-amino-3, 4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl)threonine, C(9)H(13)N(5)O(5)(5) (monoclinic, P2(1)), the C-nitroso fragments exhibit almost equal C-N and N-O bond lengths: the C-N range is 1. 315 (3)-1.329 (3) A and the N-O range is 1.293 (3)-1.326 (3) A. In each compound there are also very short intermolecular O-H.O hydrogen bonds, in which carboxyl groups act as hydrogen-bond donors to the nitrosyl O atoms: the O.O distances range from 2.440 (2) to 2. 504 (4) A and the O-H.O angles lie between 161 and 163 degrees. An interpretation of the relationship between the unusual intramolecular bond lengths and the very short intermolecular hydrogen bonds has been developed based on database analysis and computational modelling. In each of (3)-(5) there is an extensive network of intermolecular hydrogen bonds, generating three-dimensional frameworks in (3) and (5), and two-dimensional sheets in (4).

Induction of microalbuminuria by l-arginine infusion in healthy individuals: an insight into the mechanisms of proteinuria

Despite evidence from individuals with diabetes mellitus or reduced renal mass, the actual relationship between protein- or amino acid-induced changes in renal function and urinary albumin excretion (UAE) is largely unknown in subjects without renal disease. In humans, infusions of l-arginine have been used recently in vascular and renal pathophysiological studies. The present study was undertaken to analyze the mechanisms involved in a particular effect; namely, the behavior of UAE during amino acid loading. A prospective interventional protocol was performed on 10 healthy adults by means of an intravenous infusion of l-arginine. The main results show that l-arginine induced a significant increase in UAE from 13.1 +/- 3.8 before to 53.3 +/- 11.1 microgram/min after the infusion (P < 0.005). This increment was simultaneous to an increase in glomerular filtration rate (GFR) and renal plasma flow (RPF). Furthermore, l-arginine markedly increased the urinary excretion of beta2-microglobulin. UAE correlated significantly with GFR (r = 0. 738; P = 0.014) and RPF (r = 0.942; P < 0.0001), but not with urinary beta2-microglobulin (r = 0.05; P = not significant). Furthermore, marked differences (P = 0.001) were found between the percentage of increase in UAE (306.8% +/- 163.2%) with respect to either albumin filtered load (FLAlb; 57.9% +/- 16.3%) and beta2-microglobulin excretion (1,088.5% +/- 424.6%). No changes were found in vehicle-infused individuals. In conclusion, the present study shows, in controlled conditions, that l-arginine infusion induces a relevant increase in UAE in healthy individuals that significantly exceeds that expected from the increase in GFR alone. The intense and simultaneous increment in beta2-microglobulin excretion strongly suggests that the effect of l-arginine on UAE is, in a relevant part, mediated through a blockade in the tubular protein reabsorption pathways. However, the profound differences observed in the changes induced by l-arginine on UAE and beta2-microglobulin excretion and the differences in the correlation of UAE and beta2-microglobulin with respect to GFR suggest that substantial diversity exists in the mechanisms by which l-arginine affects the renal management of albumin and beta2-microglobulin. These findings are relevant for understanding the renal response to l-arginine and protein/amino acid loads.

Desmin myopathy: a multisystem disorder involving skeletal, cardiac, and smooth muscle

Myopathy associated with desmin-type intermediate filaments is an uncommon disorder of skeletal and/or cardiac muscle. The present study focuses on a 28-year-old man with generalized muscular atrophy, cardiomyopathy, and intestinal malabsorption and pseudo-obstruction. Abundant sarcoplasmic granular and filamentous aggregates that were ultrastructurally continuous with Z lines or dense bodies and exhibited intense immunostaining for desmin were present throughout the skeletal musculature, myocardium, and smooth muscle of the intestine. Moreover, neurofilament-immunoreactive axonal spheroids were identified in the spinal cord and roots. These widely distributed findings illustrate the multisystemic character of desmin myopathy, which in this instance first adds intestinal smooth muscle involvement to its already known skeletal and cardiac muscle manifestations. The additional presence of neurofilament aggregates in the spinal cord and roots constitutes an extremely rare conjunction of intermediate filament pathology of the neuromuscular system.

Giant cell myocarditis: monocytic immunophenotype of giant cells in a case associated with ulcerative colitis

Giant cell myocarditis (GCM) is a rare condition whose histologic hallmark, the multinucleate giant cell, is of debated origin (monocytic v myogenic). We report the case of a 46-year-old woman with a previous diagnosis of ulcerative colitis who rapidly deteriorated and died as the result of refractory ventricular tachyarrhythmias. Postmortem examination showed a diffuse infiltration of the myocardium by round cells and multinucleate giant cells. Immunohistochemically, round cells were demonstrated to be T lymphocytes admixed with monocytes. Multinucleate giant cells expressed monocytic markers (MAC 387, lysozyme) and were negative for muscle markers (actin, desmin, myoglobin). This case illustrates the monocytic and macrophagic nature of multinucleate giant cells and lends support to the autoimmune hypothesis of GCM by the concurrence of the latter with ulcerative colitis.

Dactyltronic acids from the sponge Dactylospongia elegans

Two new cytotoxic tetronic acid derivatives with a rearranged drimane skeleton [1a and 1b], were isolated from the sponge Dactylospongia elegans, along with smenospongic acid [3], illimaquinone [4], dactylospongenones A, B, C, and D [5], and dictyoceratin C [6]. The structures of 1a and 1b were elucidated by spectroscopic and chemical methods. Treatment of 1 with base gave smenospongic acid [3], suggesting that this latter compound is an end-product of D. elegans metabolism. A biogenetic route from furoterpenes to the tetronic acids [1a and b] and smenospongic acid [3] is proposed.

High density lipoprotein subfractions and physical activity: changes after moderate and heavy exercise training

The changes in high density lipoprotein (HDL) subfractions have been studied in 106 young healthy men after two months of physical training at a military base. Forty subjects were placed on a heavy intensity training program (HITP) with a daily average energy expenditure estimated as 3,504 Kcal, and 66 subjects followed a moderate intensity training program (MITP) with an average energy expenditure estimated as 2,942 Kcal/day. The HITP group reduced their body fat while HDL-cholesterol, HDL2-cholesterol and apoprotein (apo) A-I increased by 8.4%, 30% and 16.9% respectively (p less than 0.001). Body fat of MITP subjects did not change and HDL-cholesterol, HDL2-cholesterol and apo A-I increased by 5.6% (p less than 0.05), 17.1% (p less than 0.001) and 5.6% (p less than 0.05), respectively. The increase in serum apo A-I level was significantly higher (p less than 0.005) in the heavy intensity training group. The apo A-I/A-II ratio increased significantly in both groups (p less than 0.001), reflecting an increase in the HDL2/HDL3 ratio. This is in agreement with the significant increase in HDL2-cholesterol in both groups (p less than 0.001) with no change or decrease in HDL3-cholesterol.