Emergent RNA–RNA interactions can promote stability in a facultative phototrophic endosymbiosis

This is the final version. Available on open access from the National Academy of Sciences via the DOI in this recordData Availability: The sequence data, code, and datasets have been deposited in NCBI Sequence Read Archive, GitHub, Figshare, and Zenodo. The raw reads generated during sRNA sequencing are available on the NCBI Sequence Read Archive (accession numbers SAMN14932981 and SAMN14932982). All other datasets are available on Figshare (https://doi.org/10.6084/m9.figshare.c.4978160.v3) under the relevant headings (77). Custom scripts for sRNA read processing (https://github.com/guyleonard/paramecium, https://doi.org/10.5281/zenodo.4638888) and eDicer comparative analysis (https://github.com/fmaguire/eDicer, https://doi.org/10.5281/zenodo.4659378) are available on GitHub and archived within the Zenodo repository.Eukaryote–eukaryote endosymbiosis was responsible for the spread of chloroplast (plastid) organelles. Stability is required for the metabolic and genetic integration that drives the establishment of new organelles, yet the mechanisms that act to stabilize emergent endosymbioses—between two fundamentally selfish biological organisms—are unclear. Theory suggests that enforcement mechanisms, which punish misbehavior, may act to stabilize such interactions by resolving conflict. However, how such mechanisms can emerge in a facultative endosymbiosis has yet to be explored. Here, we propose that endosymbiont–host RNA–RNA interactions, arising from digestion of the endosymbiont population, can result in a cost to host growth for breakdown of the endosymbiosis. Using the model facultative endosymbiosis between Paramecium bursaria and Chlorella spp., we demonstrate that this mechanism is dependent on the host RNA-interference (RNAi) system. We reveal through small RNA (sRNA) sequencing that endosymbiont-derived messenger RNA (mRNA) released upon endosymbiont digestion can be processed by the host RNAi system into 23-nt sRNA. We predict multiple regions of shared sequence identity between endosymbiont and host mRNA, and demonstrate through delivery of synthetic endosymbiont sRNA that exposure to these regions can knock down expression of complementary host genes, resulting in a cost to host growth. This process of host gene knockdown in response to endosymbiont-derived RNA processing by host RNAi factors, which we term “RNAi collisions,” represents a mechanism that can promote stability in a facultative eukaryote–eukaryote endosymbiosis. Specifically, by imposing a cost for breakdown of the endosymbiosis, endosymbiont–host RNA–RNA interactions may drive maintenance of the symbiosis across fluctuating ecological conditions.European Molecular Biology OrganizationRoyal SocietyEuropean Research Council (ERC)Wellcome TrustLister InstituteDonald Hill Family Fellowshi

Characterization of the RNA-interference pathway as a tool for reverse genetic analysis in the nascent phototrophic endosymbiosis, Paramecium bursaria

This is the final version. Available on open access from the Royal Society via the DOI in this recordData accessibility The raw reads generated during transcriptome and sRNA sequencing are available on the NCBI Sequence Read Archive (accessions: SAMN14932981, SAMN14932982). All other datasets are available on Figshare (https://doi.org/10.6084/m9.figshare.c.5241983.v1), under the relevant headings. Custom scripts for host and endosymbiont transcript binning [80] (https://github.com/fmaguire/dendrogenous, https://doi.org/10.5281/zenodo.4639294) and sRNA read processing [81] (https://github.com/guyleonard/paramecium, https://doi.org/10.5281/zenodo.4638888) are available on GitHub and archived within the Zenodo repository.Endosymbiosis was fundamental for the evolution of eukaryotic complexity. Endosymbiotic interactions can be dissected through forward- and reverse-genetic experiments, such as RNA-interference (RNAi). However, distinguishing small (s)RNA pathways in a eukaryote-eukaryote endosymbiotic interaction is challenging. Here, we investigate the repertoire of RNAi pathway protein-encoding genes in the model nascent endosymbiotic system, Paramecium bursaria-Chlorella spp. Using comparative genomics and transcriptomics supported by phylogenetics, we identify essential proteome components of the small interfering (si)RNA, scan (scn)RNA and internal eliminated sequence (ies)RNA pathways. Our analyses reveal that copies of these components have been retained throughout successive whole genome duplication (WGD) events in the Paramecium clade. We validate feeding-induced siRNA-based RNAi in P. bursaria via knock-down of the splicing factor, u2af1, which we show to be crucial to host growth. Finally, using simultaneous knock-down 'paradox' controls to rescue the effect of u2af1 knock-down, we demonstrate that feeding-induced RNAi in P. bursaria is dependent upon a core pathway of host-encoded Dcr1, Piwi and Pds1 components. Our experiments confirm the presence of a functional, host-derived RNAi pathway in P. bursaria that generates 23-nt siRNA, validating the use of the P. bursaria-Chlorella spp. system to investigate the genetic basis of a nascent endosymbiosis.EMBORoyal SocietyEuropean Research Council (ERC)Wellcome TrustLister institut

Meeting the looming policy challenge of sea-level change and human migration

PRIFPRI3; ISI; 1 Fostering Climate-Resilient and Sustainable Food Supply; 5 Strengthening Institutions and GovernanceDSG

Are mice good models for human neuromuscular disease? Comparing muscle excursions in walking between mice and humans

The mouse is one of the most widely used animal models to study neuromuscular diseases and test new therapeutic strategies. However, findings from successful pre-clinical studies using mouse models frequently fail to translate to humans due to various factors. Differences in muscle function between the two species could be crucial but often have been overlooked. The purpose of this study was to evaluate and compare muscle excursions in walking between mice and humans

Survey of attitudes, materials and methods employed in endodontic treatment by general dental practitioners in North Jordan

BACKGROUND: General dental practitioners provide the majority of endodontic treatment in Jordan. The aim of this study was to gather information on the methods, materials and attitudes employed in root canal treatment by dentists in North Jordan, in order to evaluate and improve the quality of current practice. METHODS: A questionnaire was posted to all registered general dental practitioners working in private practice in Irbid Governate in North Jordan (n = 181). The questionnaire included information on methods, materials and techniques used in endodontic treatment. RESULTS: Reply rate was 72% (n = 131). The results demonstrated that only five dentists used rubber dam occasionally and not routinely. The majority used cotton rolls for isolation solely or in combination with a high volume saliva ejector (n = 116). The most widely used irrigants were sodium hypochlorite and hydrogen peroxide, which were used by 32.9% (n = 43) and 33.6% (n = 44) of the respondents, respectively. Forty eight percent of the respondents (n = 61) used the cold lateral condensation technique for canal obturation, 31.3% (n = 41) used single cone, 9.9% (n = 13) used vertical condensation and 12.2% (n = 16) used paste or cement only for the obturation. The majority used zinc oxide eugenol as a sealer (72.5%). All, but one, respondents used hand instruments for canal preparation and the technique of choice was step back (52.7%). More than 50% (n = 70) of the dentists took one radiograph for determining the working length, whilst 22.9% (n = 30) did not take any radiograph at all. Most practitioners performed treatment in three visits for teeth with two or more root canals, and in two visits for teeth with a single root canal. CONCLUSIONS: This study indicates that dentists practicing in North Jordan do not comply with international quality standards and do not use recently introduced techniques. Many clinicians never take a radiograph for determining the working length and never used rubber dam or intra-canal medicaments

Serum lipid responses to psyllium fiber: differences between pre- and post-menopausal, hypercholesterolemic women

<p>Abstract</p> <p>Background</p> <p>Cardiovascular disease is the leading cause of death in women and men. Psyllium, a soluble fiber has been known to reduce serum lipids. In this pilot study, we evaluated whether menopausal status would affect the serum lipid responses to psyllium fiber in women.</p> <p>Methods</p> <p>Eleven post-menopausal and eight pre-menopausal women with serum total cholesterol >200 mg/dL were included in the study. Subjects consumed their habitual diet and 15 g psyllium/d for 6 weeks. Psyllium was incorporated into cookies. Each cookie contained ≈5 g of psyllium fiber. Subjects ate one cookie in each meal.</p> <p>Results</p> <p>With psyllium fiber, total cholesterol concentration was significantly lower (≈5.2%, P < 0.05) in post-menopausal women but not in pre-menopausal women (≈1.3%). Also, there was a significant decrease in HDL-cholesterol in post-menopausal women (≈10.2%, P < 0.05). There were no significant changes observed in concentrations of LDL-cholesterol, triglycerides, apolipoprotein A1, and apolipoprotein B in both pre- and post-menopausal women with psyllium.</p> <p>Conclusion</p> <p>In this pilot study, post- and pre-menopausal, hypercholesterolemic women responded differently to psyllium fiber supplementation. Post-menopausal women would benefit from addition of psyllium to their diets in reducing the risk for heart diseases. The results of this study should be used with caution because the study was based on a small sample size.</p

Analysis of synonymous codon usage in Hepatitis A virus

<p>Abstract</p> <p>Background</p> <p>Hepatitis A virus is the causative agent of type A viral hepatitis, which causes occasional acute hepatitis. Nevertheless, little information about synonymous codon usage pattern of HAV genome in the process of its evolution is available. In this study, the key genetic determinants of codon usage in HAV were examined.</p> <p>Results</p> <p>The overall extent of codon usage bias in HAV is high in <it>Picornaviridae</it>. And the patterns of synonymous codon usage are quite different in HAV genomes from different location. The base composition is closely correlated with codon usage bias. Furthermore, the most important determinant that results in such a high codon bias in HAV is mutation pressure rather than natural selection.</p> <p>Conclusions</p> <p>HAV presents a higher codon usage bias than other members of <it>Picornaviridae</it>. Compositional constraint is a significant element that influences the variation of synonymous codon usage in HAV genome. Besides, mutation pressure is supposed to be the major factor shaping the hyperendemic codon usage pattern of HAV.</p

The impact of preoperative anxiety and education level on long-term mortality after cardiac surgery

<p>Abstract</p> <p>Background</p> <p>Psychosocial factors have shown independent predictive value in the development of cardiovascular diseases. Although there is strong evidence to support the role of psychosocial factors in cardiovascular mortality, there is a scarcity of knowledge about how these factors are related. Therefore, we investigated the relationship between depression, anxiety, education, social isolation and mortality 7.5 years after cardiac surgery.</p> <p>Methods</p> <p>After informed consent, 180 patients undergoing cardiac surgery between July 2000 and May 2001 were prospectively enrolled and followed for ten years. During the follow-up period, the patients were contacted annually by mail. Anxiety (Spielberger State-Trait Anxiety Inventory, STAI-S/STAI-T), depression (Beck Depression Inventory, BDI) and the number and reason for rehospitalizations were assessed each year. Those patients who did not respond were contacted by telephone, and national registries were searched for deaths.</p> <p>Results</p> <p>During a median follow-up of 7.6 years (25^th to 75^th percentile, 7.4 to 8.1 years), the mortality rate was 23.6% (95% confidence interval [CI] 17.3-29.9; 42 deaths). In a Cox regression model, the risk factors associated with an increased risk of mortality were a higher EUROSCORE (points; Adjusted Hazard Ratio (AHR):1.30, 95%CI:1.07-1.58)), a higher preoperative STAI-T score (points; AHR:1.06, 95%CI 1.02-1.09), lower education level (school years; AHR:0.86, 95%CI:0.74-0.98), and the occurrence of major adverse cardiac and cerebral events during follow up (AHR:7.24, 95%CI:2.65-19.7). In the postdischarge model, the same risk factors remained.</p> <p>Conclusions</p> <p>Our results suggest that the assessment of psychosocial factors, particularly anxiety and education may help identify patients at an increased risk for long-term mortality after cardiac surgery.</p

Malaria mosquito control using edible fish in western Kenya: preliminary findings of a controlled study

<p>Abstract</p> <p>Background</p> <p>Biological control methods are once again being given much research focus for malaria vector control. This is largely due to the emerging threat of strong resistance to pesticides. Larvivorous fish have been used for over 100 years in mosquito control and many species have proved effective. In the western Kenyan highlands the larvivorous fish <it>Oreochromis niloticus </it>L. (Perciformes: Cichlidae) (formerly <it>Tilapia nilotica</it>) is commonly farmed and eaten but has not been previously tested in the field for malaria mosquito control.</p> <p>Methods</p> <p>This fish was introduced into abandoned fishponds at an altitude of 1,880 m and the effect measured over six months on the numbers of mosquito immatures. For comparison an untreated control pond was used. During this time, all ponds were regularly cleared of emergent vegetation and fish re-stocking was not needed. Significant autocorrelation was removed from the time series data, and t-tests were used to investigate within a pond and within a mosquito type any differences before and after the introduction of <it>O. niloticus</it>. Mulla's formula was also used on the raw data to calculate the percentage reduction of the mosquito larvae.</p> <p>Results</p> <p>After <it>O. niloticus </it>introduction, mosquito densities immediately dropped in the treated ponds but increased in the control pond. This increase was apparently due to climatic factors. Mulla's formula was applied which corrects for that natural tendency to increase. The results showed that after 15 weeks the fish caused a more than 94% reduction in both <it>Anopheles gambiae s.l</it>. and <it>Anopheles funestus </it>(Diptera: Culicidae) in the treated ponds, and more than 75% reduction in culicine mosquitoes. There was a highly significantly reduction in <it>A. gambiae s.l</it>. numbers when compared to pre-treatment levels.</p> <p>Conclusion</p> <p>This study reports the first field trial data on <it>O. niloticus </it>for malaria mosquito control and shows that this species, already a popular food fish in western Kenya, is an apparently sustainable mosquito control tool which also offers a source of protein and income to people in rural areas. There should be no problem with acceptance of this malaria control method since the local communities already farm this fish species.</p