| 1. |
- Grapotte, M, et al.
(author)
-
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
- 2021
-
In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 3297-
-
Journal article (peer-reviewed)abstract
- Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
|
|
| 2. |
- Bengtsson, Sara K. S., 1978-, et al.
(author)
-
Extra-synaptic GABAA receptor potentiation and neurosteroid-induced learning deficits are inhibited by GR3027, a GABAA modulating steroid antagonist
- 2023
-
In: Biomolecules. - : MDPI. - 2218-273X. ; 13:10
-
Journal article (peer-reviewed)abstract
- Objectives In Vitro: To study the effects of GR3027 (golexanolone) on neurosteroid-induced GABA-mediated current responses under physiological GABAergic conditions with recombinant human α5β3γ2L and α1β2γ2L GABAA receptors expressed in human embryonic kidney cells, using the response patch clamp technique combined with the Dynaflow™ application system. With α5β3γ2L receptors, 0.01–3 μM GR3027, in a concentration-dependent manner, reduced the current response induced by 200 nM THDOC + 0.3 µM GABA, as well as the THDOC-induced direct gated effect. GR3027 (1 μM) alone had no effect on the GABA-mediated current response or current in the absence of GABA. With α1β2γ2L receptors, GR3027 alone had no effect on the GABA-mediated current response or did not affect the receptor by itself. Meanwhile, 1–3 µM GR3027 reduced the current response induced by 200 nM THDOC + 30 µM GABA and 3 µM GR3027 that induced by 200 nM THDOC when GABA was not present. Objectives In Vivo: GR3027 reduces allopregnanolone (AP)-induced decreased learning and anesthesia in male Wistar rats. Rats treated i.v. with AP (2.2 mg/kg) or vehicle were given GR3027 in ratios of 1:0.5 to 1:5 dissolved in 10% 2-hydroxypropyl-beta-cyclodextrin. A dose ratio of AP:GR3027 of at least 1:2.5 antagonized the AP-induced decreased learning in the Morris Water Mase (MWM) and 1:7.5 antagonized the loss of righting reflex (LoR). GR3027 treatment did not change other functions in the rat compared to the vehicle group. Conclusions: GR3027 functions in vitro as an inhibitor of GABAA receptors holding α5β3γ2L and α1β2γ2L, in vivo, in the rat, as a dose-dependent inhibitor toward AP’s negative effects on LoR and learning in the MWM.
|
|
| 3. |
- Bäckström, Torbjörn, et al.
(author)
-
Isoallopregnanolone inhibits estrus cycle-dependent aggressive behavior
- 2023
-
In: Biomolecules. - : MDPI. - 2218-273X. ; 13:6
-
Journal article (peer-reviewed)abstract
- Among female rats, some individuals show estrus cycle-dependent irritability/aggressive behaviors, and these individual rats may be used as a model for premenstrual dysphoric disorder (PMDD). We wanted to investigate if these behaviors are related to the estrus cycle phase containing moderately increased levels of positive GABA-A receptor-modulating steroids (steroid-PAM), especially allopregnanolone (ALLO), and if the adverse behavior can be antagonized. The electrophysiology studies in this paper show that isoallopregnanolone (ISO) is a GABA-A-modulating steroid antagonist (GAMSA), meaning that ISO can antagonize the agonistic effects of positive GABA-A receptor-modulating steroids in both α1β2γ2L and α4β3δ GABA-A receptor subtypes. In this study, we also investigated whether ISO could antagonize the estrus cycle-dependent aggressive behaviors in female Wistar rats using a resident–intruder test. Our results confirmed previous reports of estrus cycle-dependent behaviors in that 42% of the tested rats showed higher levels of irritability/aggression at diestrus compared to those at estrus. Furthermore, we found that, during the treatment with ISO, the aggressive behavior at diestrus was alleviated to a level comparable to that of estrus. We noticed an 89% reduction in the increase in aggressive behavior at diestrus compared to that at estrus. Vehicle treatment in the same animals showed a minimal effect on the diestrus-related aggressive behavior. In conclusion, we showed that ISO can antagonize Steroid-PAM both in α1β2γ2L and α4β3δ GABA-A receptor subtypes and inhibit estrus cycle-dependent aggressive behavior.
|
|
| 4. |
- Chin, Chui-Yoke, et al.
(author)
-
Francisella FlmX broadly affects lipopolysaccharide modification and virulence
- 2021
-
In: Cell Reports. - : Elsevier. - 2211-1247. ; 35:11
-
Journal article (peer-reviewed)abstract
- The outer membrane protects Gram-negative bacteria from the host environment. Lipopolysaccharide (LPS), a major outer membrane constituent, has distinct components (lipid A, core, O-antigen) generated by specialized pathways. In this study, we describe the surprising convergence of these pathways through FlmX, an uncharacterized protein in the intracellular pathogen Francisella. FlmX is in the flippase family, which includes proteins that traffic lipid-linked envelope components across membranes. flmX deficiency causes defects in lipid A modification, core remodeling, and O-antigen addition. We find that an F. tularensis mutant lacking flmX is >1,000,000-fold attenuated. Furthermore, FlmX is required to resist the innate antimicrobial LL-37 and the antibiotic polymyxin. Given FlmX's central role in LPS modification and its conservation in intracellular pathogens Brucella, Coxiella, and Legionella, FlmX may represent a novel drug target whose inhibition could cripple bacterial virulence and sensitize bacteria to innate antimicrobials and antibiotics.
|
|
| 5. |
- Evengård, Birgitta, 1952-, et al.
(author)
-
Healthy ecosystems for human and animal health : Science diplomacy for responsible development in the Arctic
- 2021
-
In: Polar Record. - : Cambridges Institutes Press. - 0032-2474 .- 1475-3057. ; 57
-
Journal article (peer-reviewed)abstract
- Climate warming is occurring most rapidly in the Arctic, which is both a sentinel and a driver of further global change. Ecosystems and human societies are already affected by warming. Permafrost thaws and species are on the move, bringing pathogens and vectors to virgin areas. During a five-year project, the CLINF - a Nordic Center of Excellence, funded by the Nordic Council of Ministers, has worked with the One Health concept, integrating environmental data with human and animal disease data in predictive models and creating maps of dynamic processes affecting the spread of infectious diseases. It is shown that tularemia outbreaks can be predicted even at a regional level with a manageable level of uncertainty. To decrease uncertainty, rapid development of new and harmonised technologies and databases is needed from currently highly heterogeneous data sources. A major source of uncertainty for the future of contaminants and infectious diseases in the Arctic, however, is associated with which paths the majority of the globe chooses to follow in the future. Diplomacy is one of the most powerful tools Arctic nations have to influence these choices of other nations, supported by Arctic science and One Health approaches that recognise the interconnection between people, animals, plants and their shared environment at the local, regional, national and global levels as essential for achieving a sustainable development for both the Arctic and the globe.
|
|
| 6. |
- Mohammadi, Nasibeh, 1981-
(author)
-
Determining the role of guanylate-binding proteins for host defense against Francisella tularensis
- 2022
-
Doctoral thesis (other academic/artistic)abstract
- Francisella tularensis is a highly virulent, intracellular bacterium and the causative agent of the human disease tularemia. This is a zoonotic, often vector-borne disease. Due to its intracellular nature, F. tularensis can infect many cell types, but of special relevance is its ability to infect monocytic cells and avoid their otherwise potent antimicrobial effects. Monocytic cells can; however, control infection after activation with IFN-γ, but the molecular mechanisms behind this control are not well understood. Recently, guanylate-binding proteins (GBPs) have been identified as crucial for the control of intracellular F. tularensis and many other bacteria, viruses, and parasites. They represent a vast family of interferon-inducible proteins, but it is incompletely understood how their ubiquitous abilities to control diverse types of infections are executed. The overall aim of the thesis was to obtain a better understanding of how GBPs execute the control of infection caused by Francisella and how the bacterium counteracts the bactericidal effects of the GBPs and of other immune mediators. To this end, the responses of bone marrow-derived murine macrophages (BMDM) to Francisella was one model investigated and the other employed a co-culture system whereby BMDM were infected and to the cultures immune cells from vaccinated mice were added. To comprehensively understand the host-pathogen interaction, a variety of Francisella strains were utilized; the highly virulent SCHU S4 strain, the human live vaccine strain (LVS), and the widely used surrogate for F. tularensis, the low virulent F. novicida. All strains have similar capability of intracellular multiplication in BMDM, however, activation of the microbicidal ability of BMDM with IFN-γ, significant control of infection was observed for the LVS and F. novicida strains, whereas there was no control of the SCHU S4 infection. The control of the former strains was GBP-dependent, despite that no differences in GBP transcription or translation were observed in the infected cell cultures. Patterns of 18 cytokines very clearly discriminated the different types of infections and high levels were generally observed in F. novicida-infected cultures and very low levels in SCHU S4-infected cultures. Co-infection with F. novicida and SCHU S4 led to significant control of both strains and in these cultures, a majority of cytokines showed intermediate or high levels. A critical component in the immune recognition of Francisella is AIM2, which is a core constituent of a special form of inflammasome, a cytoplasmic multimeric complex. We determined that AIM2-deficient BMDM, despite the central role of AIM2 for immune recognition of F. novicida and LVS, still controlled infection with either of the two strains after activation with IFN-γ. Again, no control of the virulent strain SCHU S4 was observed. The co-culture system revealed further complexity beyond that of the BMDM model. Utilizing splenocytes obtained from immunized C57BL/6 mice as effectors in cultures with BMDM infected with either of the three Francisella strains, we observed that regardless of strain, significant control of replication occurred with wild-type macrophages and immune splenocytes, even for the highly virulent SCHU S4 strain, but not in cultures with immune splenocytes and GBP-deficient macrophages. Supernatants from the cultures demonstrated very distinct patterns for each of the three infections. Thus, the co-culture assay identified, as for the BMDM model, a crucial role of GBPs for the control of intracellular replication of Francisella, however, in contrast to the BMDM model, the co-culture conferred significant control of SCHU S4 infection.Collectively, our studies demonstrate a very important role of GBPs for the IFN-γ-dependent control of Francisella infection, with the notable exception of the highly virulent strain SCHU S4. A GBP-mediated control of SCHU S4 was; however, observed in the co-culture system, thereby identifying additional bactericidal mechanisms, besides those that are IFN-γ-dependent. We also demonstrate that the inflammatory potential of Francisella strains is correlated to their virulence, most notable is the almost complete lack of inflammatory response during infection with the highly virulent SCHU S4 strain, but this anti-inflammatory capacity was counteracted by the strong pro-inflammatory property of F. novicida during co-infection.
|
|
