The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases

RNA polymerases (RNAPs) synthesize RNA from NTPs, whereas DNA polymerases synthesize DNA from 2dNTPs. DNA polymerases select against NTPs by using steric gates to exclude the 2 ' OH, but RNAPs have to employ alternative selection strategies. In single-subunit RNAPs, a conserved Tyr residue discriminates against 2 ' dNTPs, whereas selectivity mechanisms of multi-subunit RNAPs remain hitherto unknown. Here, we show that a conserved Arg residue uses a two-pronged strategy to select against 2 ' dNTPs in multi-subunit RNAPs. The conserved Arg interacts with the 2 ' OH group to promote NTP binding, but selectively inhibits incorporation of 2 ' dNTPs by interacting with their 3 ' OH group to favor the catalytically-inert 2 ' -endo conformation of the deoxyribose moiety. This deformative action is an elegant example of an active selection against a substrate that is a substructure of the correct substrate. Our findings provide important insights into the evolutionary origins of biopolymers and the design of selective inhibitors of viral RNAPs. RNA and DNA polymerases need to discriminate efficiently against closely related nucleotide triphosphate substrates. Here, the authors show that a conserved Arg residue is the major determinant of selectivity against deoxyribonucleoside substrates by multisubunit RNA polymerases

The role of the maleimide ring system on the structure-activity relationship of showdomycin

Showdomycin produced by Streptomyces showdoensis ATCC 15227 is a C-nucleoside microbial natural product with antimicrobial and cytotoxic properties. The unique feature of showdomycin in comparison to other nucleosides is its maleimide base moiety, which has the distinct ability to alkylate nucleophilic thiol groups by a Michael addition reaction. In order to understand structure-activity relationships of showdomycin, we synthesized a series of derivatives with modifications in the maleimide ring at the site of alkylation to moderate its reactivity. The showdomycin congeners were designed to retain the planarity of the base ring system to allow Watson-Crick base pairing and preserve the nucleosidic character of the compounds. Consequently, we synthesized triphosphates of showdomycin derivatives and tested their activity against RNA polymerases. Bromo, methylthio, and ethylthio derivatives of showdomycin were incorporated into RNA by bacterial and mitochondrial RNA polymerases and somewhat less efficiently by the eukaryotic RNA polymerase II. Showdomycin derivatives acted as uridine mimics and delayed further extension of the RNA chain by multi-subunit, but not mitochondrial RNA polymerases. Bioactivity profiling indicated that the mechanism of action of ethylthioshowdomycin was altered, with approximately 4-fold reduction in both cytotoxicity against human embryonic kidney cells and antibacterial activity against Escherichia coli. In addition, the ethylthio derivative was not inactivated by medium components or influenced by addition of uridine in contrast to showdomycin. The results explain how both the maleimide ring and the nucleoside nature contribute to the bioactivity of showdomycin and demonstrates for the first time that the two activities can be separated.</p

Planetary well-being

Tensions between the well-being of present humans, future humans, and nonhuman nature manifest in social protests and political and academic debates over the future of Earth. The increasing consumption of natural resources no longer increases, let alone equalises, human well-being, but has led to the current ecological crisis and harms both human and nonhuman well-being. While the crisis has been acknowledged, the existing conceptual frameworks are in some respects ill-equipped to address the crisis in a way that would link the resolving of the crisis with the pivotal aim of promoting equal well-being. The shortcomings of the existing concepts in this respect relate to anthropocentric normative orientation, methodological individualism that disregards process dynamics and precludes integrating the considerations of human and nonhuman well-being, and the lack of multiscalar considerations of well-being. This work derives and proposes the concept of planetary well-being to address the aforementioned conceptual issues, to recognise the moral considerability of both human and nonhuman well-being, and to promote transdisciplinary, cross-cultural discourse for addressing the crisis and for promoting societal and cultural transformation. Conceptually, planetary well-being shifts focus on well-being from individuals to processes, Earth system and ecosystem processes, that underlie all well-being. Planetary well-being is a state where the integrity of Earth system and ecosystem processes remains unimpaired to a degree that species and populations can persist to the future and organisms have the opportunity to achieve well-being. After grounding and introducing planetary well-being, this work shortly discusses how the concept can be operationalised and reflects upon its potential as a bridging concept between different worldviews.</p

Monitoring of ticks and tick-borne pathogens through a nationwide research station network in Finland

In 2015 a long-term, nationwide tick and tick-borne pathogen (TBP) monitoring project was started by the Finnish Tick Project and the Finnish Research Station network (RESTAT), with the goal of producing temporally and geographically extensive data regarding exophilic ticks in Finland. In the current study, we present results from the first four years of this collaboration. Ticks were collected by cloth dragging from 11 research stations across Finland in May–September 2015–2018 (2012–2018 in Seili). Collected ticks were screened for twelve different pathogens by qPCR: Borrelia afzelii, Borrelia garinii, Borrelia valaisiana, Borrelia burgdorferi sensu stricto, Borrelia miyamotoi, Babesia spp., Anaplasma phagocytophilum, Rickettsia spp., Candidatus Neoehrlichia mikurensis, Francisella tularensis, Bartonella spp. and tick-borne encephalitis virus (TBEV). Altogether 15 067 Ixodes ricinus and 46 Ixodes persulcatus were collected during 68 km of dragging. Field collections revealed different seasonal activity patterns for the two species. The activity of I. persulcatus adults (only one nymph detected) was unimodal, with activity only in May–July, whereas Ixodes ricinus was active from May to September, with activity peaks in September (nymphs) or July–August (adults). Overall, tick densities were higher during the latter years of the study. Borrelia burgdorferi sensu lato were the most common pathogens detected, with 48.9 ± 8.4% (95% Cl) of adults and 25.3 ± 4.4% of nymphs carrying the bacteria. No samples positive for F. tularensis, Bartonella or TBEV were detected. This collaboration project involving the extensive Finnish Research Station network has ensured enduring and spatially extensive, long-term tick data collection to the foreseeable future

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

New susceptibility loci associated with kidney disease in type 1 diabetes

WOS:000309817900008Diabetic kidney disease, or diabetic nephropathy (DN), is a major complication of diabetes and the leading cause of end-stage renal disease (ESRD) that requires dialysis treatment or kidney transplantation. In addition to the decrease in the quality of life, DN accounts for a large proportion of the excess mortality associated with type 1 diabetes (T1D). Whereas the degree of glycemia plays a pivotal role in DN, a subset of individuals with poorly controlled T1D do not develop DN. Furthermore, strong familial aggregation supports genetic susceptibility to DN. However, the genes and the molecular mechanisms behind the disease remain poorly understood, and current therapeutic strategies rarely result in reversal of DN. In the GEnetics of Nephropathy: an International Effort (GENIE) consortium, we have undertaken a meta-analysis of genome-wide association studies (GWAS) of T1D DN comprising ∼2.4 million single nucleotide polymorphisms (SNPs) imputed in 6,691 individuals. After additional genotyping of 41 top ranked SNPs representing 24 independent signals in 5,873 individuals, combined meta-analysis revealed association of two SNPs with ESRD: rs7583877 in the AFF3 gene (P = 1.2×10(-8)) and an intergenic SNP on chromosome 15q26 between the genes RGMA and MCTP2, rs12437854 (P = 2.0×10(-9)). Functional data suggest that AFF3 influences renal tubule fibrosis via the transforming growth factor-beta (TGF-β1) pathway. The strongest association with DN as a primary phenotype was seen for an intronic SNP in the ERBB4 gene (rs7588550, P = 2.1×10(-7)), a gene with type 2 diabetes DN differential expression and in the same intron as a variant with cis-eQTL expression of ERBB4. All these detected associations represent new signals in the pathogenesis of DN.Peer reviewe

Information needs, barriers and incentives to adopting climate change mitigation and adaptation actions in boreal agriculture

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Pyroligneous acids of differently pretreated hybrid aspen biomass:herbicide and fungicide performance

Abstract The pyroligneous acids (PAs) of woody biomass produced by torrefaction have pesticidal properties. Thus, PAs are potential alternatives to synthetic plant protection chemicals. Although woody biomass is a renewable feedstock, its use must be efficient. The efficiency of biomass utilization can be improved by applying a cascading use principle. This study is novel because we evaluate for the first time the pesticidal potential of PAs derived from the bark of hybrid aspen (Populus tremula L. × Populus tremuloides Michx.) and examine simultaneously how the production of the PAs can be interlinked with the cascade processing of hybrid aspen biomass. Hybrid aspen bark contains valuable extractives that can be separated before the hemicellulose is thermochemically converted into plant protection chemicals. We developed a cascade processing scheme, where these extractives were first extracted from the bark with hot water (HWE) or with hot water and alkaline alcohol (HWE+AAE) prior to their conversion into PAs by torrefaction. The herbicidal performance of PAs was tested using Brassica rapa as the test species, and the fungicidal performance was proven using Fusarium culmorum. The pesticidal activities were compared to those of the PAs of debarked wood and of commercial pesticides. According to the results, extractives can be separated from the bark without overtly diminishing the weed and fungal growth inhibitor performance of the produced PAs. The HWE of the bark before its conversion into PAs appeared to have an enhancing effect on the herbicidal activity. In contrast, HWE+AAE lowered the growth inhibition performance of PAs against both the weeds and fungi. This study shows that hybrid aspen is a viable feedstock for the production of herbicidal and fungicidal active chemicals, and it is possible to utilize biomass according to the cascading use principle

Parity associates with chromosomal damage in uterine leiomyomas

Mechanical forces in a constrained cellular environment were recently established as a facilitator of chromosomal damage. Whether this could contribute to tumorigenesis is not known. Uterine leiomyomas are common neoplasms that display relatively few chromosomal aberrations. We hypothesized that if mechanical forces contribute to chromosomal damage, signs of this could be seen in uterine leiomyomas from parous women. We examined the karyotypes of 1946 tumors, and found a striking overrepresentation of chromosomal damage associated with parity. We then subjected myometrial cells to physiological forces similar to those encountered during pregnancy, and found this to cause DNA breaks and a DNA repair response. While mechanical forces acting in constrained cellular environments may thus contribute to neoplastic degeneration, and genesis of uterine leiomyoma, further studies are needed to prove possible causality of the observed association. No evidence for progression to malignancy was found. Many factors have been associated with chromosomal damage, including mechanical forces in a constrained cellular environment. Here the authors reveal an association between parity and chromosomal damage by analysing karyotypes of 1946 uterine leiomyomas.Peer reviewe