Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.Peer reviewe

Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.

In the version of this article initially published, there was a mistake in the calculation of the nucleotide mutation rate per site per generation: 1 × 10−9 mutations per site per generation was used, whereas 9.5 × 10−9 was correct. This error affects the interpretation of population-size changes over time and their possible correspondence with known geological events, as shown in the original Fig. 4 and supporting discussion in the text, as well as details in the Supplementary Note. Neither the data themselves nor any other results are affected. Figure 4 has been revised accordingly. Images of the original and corrected figure panels are shown in the correction notice

Terpenoidide emissooni füsioloogilised ja molekulaarsed kontrollmehhanismid tomati (Solanum lycopersicum) ja h. raudrohu (Achillea millefolium) näidetel

Thesis applying for the degree of Doctor of Philosophy in AgricultureRising temperature have a profound impact on many natural ecosystems worldwide. During the last 100 years, global temperature has been increased by 0.76◦C per year as a result of increasing concentrations of greenhouse gases due to burning of fossil fuels and deforestation. Besides, the high temperature and also cold temperature have a substantial impact on plant physiology including photosynthetic attributes, production and emission of volatile terpenoids. The effects of heat stress depend on the severity of heat and cold stress (mild or severe) that resulted in reversible or irreversible inhibition of foliage photosynthetic characteristics, volatile terpenoid emission, and regulation of terpene synthase gene expression. The main goal of this thesis was to investigate the effects of cold and heat stress on leaf photosynthesis, volatile terpenoid emissions, expression of two candidate terpene synthase genes in tomato. In this study, foliage photosynthesis characteristics and emission of volatile terpenoids are reduced after heat and cold stress and it was also found that expression of terpenoid synthase genes was altered in response to mild and severe heat stress. In addition, amplification of germacrene A synthase gene was the first report of this gene in yarrow which was functionally characterized and quantified in different tissues of yarrow in order to understand how terpenes are regulated in gene level in a model plant. Finally, it was also demonstrated that terpene synthases can accept different substrates to form different terpene products mainly based on availability of substrates. These multi substrate enzymes are more common in plants than generally thought and therefore it is highly recommended further studies be carried out to understand the existence of the terpene synthase enzyme capacity for multi-substrate use across plant kingdom.Temperatuuri tõusul on oluline mõju looduslikele ökosüsteemidele üle maailma. Kasvuhoonegaaside kontsentratsiooni tõusu ning metsade pindala vähenemise tõttu on viimase 100 aasta jooksul on globaalne temperatuur tõusnud 0.76°C aastas. Lisaks sellele mõjutavad nii kõrged kui madalad temperatuurid olulisel määral taime füsioloogiat, sealhulgas fotosünteesi parameetreid ja lenduvate terpenoidide tootmist ning emissiooni. Mõju ulatus oleneb nii kuuma- kui külmastressi puhul stressi tugevusest (mõõdukas või tugev), vastavalt sellele on muutused fotosünteesi parameetrites, lenduvate terenoidide eritumises ja terpeeni süntaasi geeni ekspressioonis kas tagasipöörduvad või pöördumatud. Töö peamiseks eesmärgiks oli uurida külma- ja kuumastressi mõju lehe fotosünteesile, lenduvate terpenoidide emissioonile ja kahe võimaliku terpeeni süntaasi geeni ekspressioonile. Selgub, et fotosüntees lehtedes ja lenduvate terpenoidide emissioon vähenesid nii külma- kui kuumastressi tõttu ning terpenoidide süntaasi geenide ekspressioon muutus nii mõõduka kui tugeva stressi tagajärjel. Lisaks sellele amplifitseeriti esmakordselt germakreeen A süntaasi geen raudrohul ning kirjeldati geeni funktsiooni ja määrati selle rohkus erinevates taimeosades, et mõista mudeltaimes terpeenide regulatsiooni geeni tasemel. Lõpuks näidati, et terpeeni süntaasid võivad olenevalt ainete kättesaadavusest kasutada mitmeid erinevaid substraate ja toota vastavalt sellele ka erinevaid produkte. Sellised multi-substraatseid ensüüme leidub taimedes rohkem kui varasemalt arvati ja seetõttu oleksid vajalikud edasised uuringud taimeriigis laiemalt, mõistmaks paremini terpeeni süntaasi võimekust kasutada mitmeid erinevaid substraate.Publication of this thesis is supported by Estonian University of Life Sciences. This study was supported by the Estonian Ministry of Science and Education (institutional grant IUT-8-3), the European Commission through the European Regional Development Fund (Center of Excellence EcolChange, TK 131), and the European Research Council (advanced grant 322603, SIP-VOL+)

Multi-substrate terpene synthases: their occurrence and physiological significance

Terpene synthases are responsible for synthesis of a large number of terpenes in plants using substrates provided by two distinct metabolic pathways, the mevalonate-dependent pathway that is located in cytosol and has been suggested to be responsible for synthesis of sesquiterpenes (C15), and 2-C-methyl-D-erythritol-4-phosphate pathway located in plastids and suggested to be responsible for the synthesis of hemi- (C5), mono- (C10) and diterpenes (C20). Recent advances in characterization of genes and enzymes responsible for substrate and end product biosynthesis as well as efforts in metabolic engineering have demonstrated existence of a number of multi-substrate terpene synthases. This review summarizes the progress in the characterization of such multi-substrate terpene synthases and suggests that the presence of multi-substrate use might have been significantly underestimated. Multi-substrate use could lead to important changes in terpene product profiles upon substrate profile changes under perturbation of metabolism in stressed plants as well as under certain developmental stages. We therefore argue that multi-substrate use can be significant under physiological conditions and can result in complicate modifications in terpene profiles

Temporal regulation of terpene synthase gene expression in Eucalyptus globulus leaves upon ozone and wounding stresses: relationships with stomatal ozone uptake and emission responses

© 2018 Elsevier B.V. Ozone and wounding are key abiotic factors but, their interactive effects on temporal changes in terpene synthase gene expression and emission responses are poorly understood. Here, we applied combined acute ozone and wounding stresses to the constitutive isoprenoid-emitter Eucalyptus globulus and studied how isoprene, 1,8-cineole, and isoledene synthase genes were regulated, and how the gene expression was associated with temporal changes in photosynthetic characteristics, product emission rates, and stomatal ozone uptake through recovery phase. Photosynthetic characteristics and emission rate of isoprene, 1,8-cineole, and isoledene were synergistically altered, while three TPS gene expressions were antagonistically altered by combined stress applications. A time-delay analysis indicated that the best correspondences between gene expression and product emission rates were observed for 0 h time-shift for wounding and 0–2 h time-shifts for separate ozone, and combined ozone and wounding treatments. The best correspondence between ozone uptake and gene expression was observed for 0–4 h time-shifts for separate ozone and combined ozone and wounding treatments. Overall, this study demonstrated that expression profiles of isoprene, the monoterpene 1,8-cineole, and the sesquiterpene isoledene synthase genes differentially influenced their corresponding product emissions for separate and combined ozone and wounding treatments through recovery

Effect of preoperative education on recovery time of laparoscopic cholecystectomy: a randomized clinical trial

Background: Nowadays, new methods are emerging each month for a better operation with fewer complications. Laparoscopic surgery have remarkable advantages, Compared to open, such as smaller incision, less manipulation of the digestive system, less postoperative pain, fewer wound complication and faster discharge from the hospital. Therefore it is preferred by patients and surgeons and is replacing the traditional open surgical methods. However, any operation causes significant panic for patients and lack of knowledge about the surgical method is found to cause poor surgical outcomes, such as recovery time after the surgery we evaluated the effect of preoperative education on the recovery time of laparoscopic cholecystectomy candidates. Methods: This randomized clinical control trial was performed at Imam Khomeini and Alborz Hospitals in Karaj from February 2010 till January 2011. Using randomized sampling method, 100 female candidates for laparoscopic cholecystectomy were divided into two equal groups of case and control. The case group received detailed information about operating room’s condition, surgical equipment, anesthesia method, advantages and disadvantages of laparoscopic procedures, and patient’s role in self-care at recovery, whilst the control group received no education before the surgery. The two groups were compared regarding recovery time based on Aldrete modified checklist and mean time to reach the Aldrete consciousness score of 9 and the incidence of nausea was assessed among them. Results: The analysis showed that there was a significant difference between the mean time to reach Aldrete consciousness modified checklist score of 9 between the case and control group (18.04±3.87 vs. 29.66±5.44, respectively, P<0.001), therefore the case group had shorter recovery time than the control group. 10 of the case group (20%) and 3 of the control group (6%) had nausea after recovery (P=0.037, OR=0.255 (CI 95%: 0.066-0.992)). Conclusion: Preoperative education of patients can significantly decrease the recovery time after laparoscopic cholecystectomy surgery. Therefore, it is strongly recommended to include the preoperative education in routine care of laparoscopic cholecystectomy patients for better surgical outcomes

Penrose Drain Migration After Laparoscopic Surgery

Laparoscopy has made a revolution in surgical procedures and treatment of various diseases but its complications are still under investigation. Intra-abdominal visceral and vessel injuries, trocar site hernia, and leaving foreign bodies into the peritoneal cavity are among some laparoscopic surgery complications. This is a rare report of Penrose drain migration following incomplete laparoscopic Fundoplication surgery. The patient was a 47- year- old woman, who was a candidate for Touplet Fundoplication via laparoscopic approach due to refractory gastro-esophageal reflux disease (GERD). While wrapping a Penrose drain around the esophagus, the patient had a cardiorespiratory arrest. Attempts to remove the Penrose drain were unsuccessful and the surgical procedure was terminated due to patient&apos;s condition. Four months later, after a long period of dysphagia and abdominal pain, the Penrose drain was defecated via rectum

Comparative Phenotyping of Two Commonly Used Chlamydomonas reinhardtii Background Strains: CC-1690 (21gr) and CC-5325 (The CLiP Mutant Library Background)

The unicellular green alga Chlamydomonas reinhardtii is an excellent model organism to investigate many essential cellular processes in photosynthetic eukaryotes. Two commonly used background strains of Chlamydomonas are CC-1690 and CC-5325. CC-1690, also called 21gr, has been used for the Chlamydomonas genome project and several transcriptome analyses. CC-5325 is the background strain for the Chlamydomonas Library Project (CLiP). Photosynthetic performance in CC-5325 has not been evaluated in comparison with CC-1690. Additionally, CC-5325 is often considered to be cell-wall deficient, although detailed analysis is missing. The circadian rhythms in CC-5325 are also unclear. To fill these knowledge gaps and facilitate the use of the CLiP mutant library for various screens, we performed phenotypic comparisons between CC-1690 and CC-5325. Our results showed that CC-5325 grew faster heterotrophically in dark and equally well in mixotrophic liquid medium as compared to CC-1690. CC-5325 had lower photosynthetic efficiency and was more heat-sensitive than CC-1690. Furthermore, CC-5325 had an intact cell wall which had comparable integrity to that in CC-1690 but appeared to have reduced thickness. Additionally, CC-5325 could perform phototaxis, but could not maintain a sustained circadian rhythm of phototaxis as CC1690 did. Finally, in comparison to CC-1690, CC-5325 had longer cilia in the medium with acetate but slower swimming speed in the medium without nitrogen and acetate. Our results will be useful for researchers in the Chlamydomonas community to choose suitable background strains for mutant analysis and employ the CLiP mutant library for genome-wide mutant screens under appropriate conditions, especially in the areas of photosynthesis, thermotolerance, cell wall, and circadian rhythms