Biology subjects

Salminen, P.

Publications and source records attributed to Salminen, P..

6 recordsLinked to original sources

bioRxiv2026

Spontaneous mutation rate in Saccharomyces cerevisiae is lower in nutritional and genotypic conditions reducing specific growth rate

Even in the absence of mutagenic factors, spontaneous errors in DNA replication generate genetic diversity in microbial populations. The spontaneous mutation rate is not immutable but may be conditionally elevated. However, it remains unresolved whether apparently non-stressful nutritional or genotypic conditions affect the spontaneous mutation rate. Here, we determined the spontaneous mutation rate of haploid Saccharomyces cerevisiae CEN.PK113-7D in three nutritional and three genotypic conditions. The nutritional and genotypic conditions influenced the specific growth rate of the S. cerevisiae population. Thus, we extended the established fluctuation assay for spontaneous mutation rate determination with CAN1 as a reporter gene to populations with different generation times. We applied the method to determine the spontaneous mutations rates in wild type S. cerevisiae grown on glucose and ammonium, raffinose and ammonium, and glucose and L-tryptophan as sole carbon and nitrogen sources. Alike we determined the spontaneous mutation rates of two engineered S. cerevisiae strains (i.e., representing genotypic conditions different from wild type) on glucose and ammonium medium. The engineered strains had two to three heterologous or variant genes integrated into the genome, common to simple heterologous small molecule production host strains. In all alternative nutritional and genotypic conditions, the spontaneous mutation rate of S. cerevisiae was reduced compared to wild type growing on glucose and ammonium medium. Spontaneous mutation rate is fundamentally relevant for evolvability of strains, but it may also influence the performance robustness of microbial populations in applications such as food or beverage fermentation or biotechnological chemical production. Our novel findings are important for biotechnological processes using microbial cells, often engineered and cultivated in unnatural chemical environments.

evolutionary biology↗

bioRxiv2025

Longitudinal dynamics of gut plasmidome and antibiotic resistance during antibiotic therapy: a case report

The human gut microbiome is composed of diverse microbes, and its association with human health is well-recognized. Antibiotic therapies for treating infectious diseases often mediate adverse influences on gut microbial ecosystems. Further, ESBL (extended-spectrum beta-lactamase)-producing bacteria potentially residing in the gut benefit from antibiotic-induced environmental changes via positive selection for resistance traits. As antimicrobial resistance (AMR) genes are often harbored by mobile plasmids, the importance of these extrachromosomal mobile genetic elements during antibiotic exposure is evident. However, there is still a knowledge gap in how microbiomes respond to antibiotic treatment especially in terms of plasmid carriage and how gut plasmid populations evolve following and revive after antibiotic therapy. To address these questions, in this case report we investigated the changes in plasmid population in the gut microbiome of a single ESBL-carrying patient during antibiotic therapy for uncomplicated acute appendicitis. Employing longitudinal sampling, we collected E. coli strains and performed metagenomic analysis before, during, and after the treatment. Our findings indicate that the antibiotic treatment is associated with a transient alteration in the microbial composition, AMR profile, and plasmid population. An extensive but temporary domination of ESBL-E. coli within the gut microbiome was observed parallel to the ongoing antibiotic treatment. However, this was not sustained in the follow-up period, indicating a slight restoration of both the microbial composition and the plasmid population. The research underscores the temporary impact of antibiotic therapy on the dynamics of the gut plasmidome which essentially mediate the spread of AMR within the gut microbiome.

microbiology↗

bioRxiv2024

Altered spike dynamics drives immune evasion of SARS-CoV-2

Escape from protective immunity has been a defining feature of the COVID-19 pandemic and is widely attributed to mutations in neutralizing antibody epitopes within the receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein. We investigated whether this paradigm accounts for the escape of Omicron lineage viruses from broadly neutralizing antibodies (bNAbs) targeting conserved RBD epitopes. We found that mutational erosion of bNAb binding epitopes was not a major driver of Omicron immune escape. Viruses carrying RBDs from highly resistant contemporary Omicron variants were potently neutralized by bNAbs when those RBDs were placed into an ancestral Wuhan-like spike backbone. Similarly, sera collected during the pre-Omicron era from individuals vaccinated with Wuhan-based vaccines retained robust RBD-specific neutralizing activity against these chimeric viruses. Mechanistically, bNAb treatment triggered exposure of the S2 cleavage site in neutralization-sensitive but not resistant spike proteins, indicating that bNAb susceptibility reflects differences in spike propensity for antibody-induced premature conformational transition. These findings show that, rather than escaping through mutation of bNAb epitopes, SARS-CoV-2 has evolved spike variants with altered conformational dynamics that resist bNAb-induced destabilization of the prefusion spike trimer.

immunology↗

bioRxiv2022

ErbB Signalling is a Potential Therapeutic Target for Vascular Lesions with Fibrous Component

BackgroundSporadic venous malformation (VM) and angiomatosis of soft tissue (AST) are benign, congenital vascular anomalies affecting venous vasculature. Depending on the size and location of the lesion, symptoms vary from motility disturbances to pain and disfigurement. Due to high recurrence of the lesions more effective therapies are needed. MethodsAs targeting stromal cells has been an emerging concept in anti-angiogenic therapies, here, by using VM/AST patient samples, RNA-sequencing, cell culture techniques and a xenograft mouse model, we investigated the crosstalk of endothelial cells (EC) and fibroblasts and its effect on vascular lesion growth. ResultsWe report, for the first time, expression and secretion of transforming growth factor A (TGFA) in ECs or intervascular stromal cells in AST and VM lesions. TGFA induced secretion of VEGF-A paracrinally, and regulated EC proliferation. Oncogenic PIK3CA variant in p.H1047R, a common somatic mutation found in these lesions, increased TGFA expression, enrichment of hallmark hypoxia, and in a mouse xenograft model, lesion size and vascularization. Treatment with afatinib, a pan-ErbB tyrosine-kinase inhibitor, decreased vascularization and lesion size in mouse xenograft model with ECs expressing oncogenic PIK3CA p.H1047R variant and fibroblasts. ConclusionsBased on the data, we suggest that targeting of both intervascular stromal cells and ECs is a potential treatment strategy for vascular lesions having a fibrous component. FundingAcademy of Finland, Ella and Georg Ehnrooth foundation, the ERC grants, Sigrid Juselius Foundation, Finnish Foundation for Cardiovascular Research, Jane and Aatos Erkko Foundation, and Department of Musculosceletal and Plastic Surgery, Helsinki University Hospital. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/509204v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@14ec94aorg.highwire.dtl.DTLVardef@1812747org.highwire.dtl.DTLVardef@39d01eorg.highwire.dtl.DTLVardef@18e9e35_HPS_FORMAT_FIGEXP M_FIG Graphical abstract. Proposed model for the paracrine signaling of TGFA/VEGF-A in vascular lesion Schematic illustration showing the general structure of venous malformation or angiomatosis of soft tissue. Pathological vasculature in the lesion (dark blue) is surrounded by disorganized extracellular matrix (ECM) and intervascular stromal cells (SCs, orange). High magnification from the area close to vessel wall demonstrates the proposed model for crosstalk between endothelial cells (ECs) and SCs. A mutation in phosphatidylinositol-4,5-biphosphate 3-kinase catalytic subunit alpha (PIK3CA) gene (1) or other processes promote ECs to express high level of transforming growth factor A (TGFA) (2). TGFA binds to epithelial growth factor receptor (EGFR) on the surface of adjacent SCs (3). Activated EGFR-downstream signaling (4) promotes elevated expression of vascular endothelial growth factor (VEGF)-A in SCs and increases the expression of TGFA (5). VEGF-A secreted from SCs (6) binds to VEGF-recetor-2 (VEGFR2) on surface of ECs (7) and together with TGFA activates angiogenic EC phenotype. TGFA secreted from the SCs (8), can further activate EGFR and its downstream signaling. C_FIG

cell biology↗

bioRxiv2021

Intranasal inhibitor blocks Omicron and other variants of SARS-CoV-2

The recent emergence of novel SARS-CoV-2 variants capable of efficiently escaping neutralizing antibodies emphasizes the need for prophylactic strategies to complement vaccination in fighting the COVID-19 pandemic. Nasal epithelium is rich in the ACE2 receptor and important for SARS-CoV-2 transmission by supporting early viral replication before seeding to the lung1. Intranasal administration of SARS-CoV-2 neutralizing antibodies or antibody fragments has shown encouraging potential as a protective measure in animal models2-5. However, there remains a dire need for SARS-CoV-2 blocking agents that are less vulnerable to mutational variation in the neutralization epitopes of the viral spike glycoprotein and more economical to produce in large scale. Here we describe TriSb92, a highly manufacturable and extremely stable trimeric human SH3 domain-derived antibody mimetic targeted against a conserved region in the receptor-binding domain of spike. TriSb92 potently neutralizes SARS-CoV-2 and its variants of concern, including Omicron BA.5 as well as the latest and most immunoevasive variants like BF.7, XBB, and BQ.1.1. Intranasal administration of a modest dose of TriSb92 (5 or 50 micrograms) as early as eight hours before a challenge with SARS-CoV-2 efficiently protected mice from infection, and was still effective even when given 4 h after the viral challenge. The target epitope of TriSb92 was defined by cryo-EM, which revealed triggering of a conformational shift in the spike trimer rather than competition for ACE2 binding as the molecular basis of its strong inhibitory action. The high potency and robust biochemical properties of TriSb92 together with the remarkable resistance of its inhibitory action against viral sequence evolution suggest that TriSb92 could be useful as a nasal spray for protecting susceptible individuals from SARS-CoV-2 infection.

microbiology↗

bioRxiv2020

Mesolimbic opioid-dopamine interaction is disrupted in obesity but recovered by weight loss following bariatric surgery

BackgroundObesity is a growing burden to health and economy worldwide. Obesity is associated with central -opioid receptor (MOR) downregulation, and the interaction between MOR and dopamine D2 receptor (D2R) system in the ventral striatum is disrupted among obese subjects. Weight loss recovers MOR function, but it remains unknown whether it also recovers aberrant opioid-dopamine interaction. Here we addressed this issue by studying subjects undergoing surgical weight loss (bariatric surgery) procedure. MethodsWe recruited 20 healthy non-obese (mean BMI 22) and 25 morbidly obese women (mean BMI 41) eligible for bariatric surgery. Brain MOR and D2R availability was measured using positron emission tomography (PET) with [11C]carfentanil and [11C]raclopride, respectively. Either Roux-en-Y gastric bypass or sleeve gastrectomy was performed to obese subjects according to standard clinical treatment. 21 obese subjects participated in the postoperative PET scanning six months after bariatric surgery. ResultsIn the control subjects, MOR and D2R availabilities were associated in the ventral striatum (r = .62) and dorsal caudate (r = .61). Preoperatively, the obese subjects had disrupted association in the ventral striatum (r = .12) but unaltered association in dorsal caudate (r = .43). The association between MOR and D2R availabilities in the ventral striatum was recovered (r = .62) among obese subjects following the surgery-induced weight loss (mean total weight loss 22 %). ConclusionsBariatric surgery and concomitant weight loss recovers the interaction between MOR and D2R in the ventral striatum in the morbidly obese. Consequently, the dysfunctional opioid-dopamine interaction in the ventral striatum is likely associated with an obese phenotype and may mediate excessive energy uptake. Striatal opioid-dopamine interaction provides a feasible target for pharmacological and behavioural interventions for treating obesity. Clinical Trials RegistrationSleevePET2, NCT01373892, http://www.clinicaltrials.gov

neuroscience↗