Nuclear phytochrome a signaling promotes phototropism in Arabidopsis.

Phototropin photoreceptors (phot1 and phot2 in Arabidopsis thaliana) enable responses to directional light cues (e.g., positive phototropism in the hypocotyl). In Arabidopsis, phot1 is essential for phototropism in response to low light, a response that is also modulated by phytochrome A (phyA), representing a classical example of photoreceptor coaction. The molecular mechanisms underlying promotion of phototropism by phyA remain unclear. Most phyA responses require nuclear accumulation of the photoreceptor, but interestingly, it has been proposed that cytosolic phyA promotes phototropism. By comparing the kinetics of phototropism in seedlings with different subcellular localizations of phyA, we show that nuclear phyA accelerates the phototropic response, whereas in the fhy1 fhl mutant, in which phyA remains in the cytosol, phototropic bending is slower than in the wild type. Consistent with this data, we find that transcription factors needed for full phyA responses are needed for normal phototropism. Moreover, we show that phyA is the primary photoreceptor promoting the expression of phototropism regulators in low light (e.g., PHYTOCHROME KINASE SUBSTRATE1 [PKS1] and ROOT PHOTO TROPISM2 [RPT2]). Although phyA remains cytosolic in fhy1 fhl, induction of PKS1 and RPT2 expression still occurs in fhy1 fhl, indicating that a low level of nuclear phyA signaling is still present in fhy1 fhl

Exosomal cancer immunotherapy is independent of MHC molecules on exosomes

Peptide-loaded exosomes are promising cancer treatment vehicles; however, moderate T cell responses in human clinical trials indicate a need to further understand exosome-induced immunity. We previously demonstrated that antigen-loaded exosomes carry whole protein antigens and require B cells for inducing antigen-specific T cells. Therefore, we investigated the relative importance of exosomal major histocompatibility complex (MHC) class I for the induction of antigen-specific T cell responses and tumour protection. We show that ovalbumin-loaded dendritic cell-derived exosomes from MHCI-/- mice induce antigen-specific T cells at the same magnitude as wild type exosomes. Furthermore, exosomes lacking MHC class I, as well as exosomes with both MHC class I and II mismatch, induced tumour infiltrating T cells and increased overall survival to the same extent as syngeneic exosomes in B16 melanoma. In conclusion, T cell responses are independent of exosomal MHC/peptide complexes if whole antigen is present. This establishes the prospective of using impersonalised exosomes, and will greatly increase the feasibility of designing exosome-based vaccines or therapeutic approaches in humans

Genomic landscape of pleural and peritoneal mesothelioma tumours

BACKGROUND Malignant pleural and peritoneal mesotheliomas are rare malignancies with unacceptable poor prognoses and limited treatment options. The genomic landscape is mainly characterised by the loss of tumour suppressor genes and mutations in DNA repair genes. Currently, data from next-generation sequencing (NGS) of mesothelioma tumours is restricted to a limited number of cases; moreover, data comparing molecular features of mesothelioma from the pleural and peritoneal origin with NGS are lacking. METHODS We analysed 1113 pleural mesothelioma and 355 peritoneal mesothelioma samples. All tumours were sequenced with the FoundationOne® or FoundationOne®CDx assay for detection of substitutions, insertion-deletions, copy-number alterations and selected rearrangements in at least 324 cancer genes. RESULTS This analysis revealed alterations in 19 genes with an overall prevalence of at least 2%. Alterations in BAP1, CDKN2A, CDKN2B, NF2, MTAP, TP53 and SETD2 occurred with a prevalence of at least 10%. Peritoneal, compared to pleural mesothelioma, was characterised by a lower prevalence of alterations in CDKN2A, CDKN2B and MTAP. Moreover, we could define four distinct subgroups according to alterations in BAP1 and CDKN2A/B. Alterations in Hedgehog pathway-related genes (PTCH1/2 and SUFU) and Hippo pathway-related gene (NF2) as well as KRAS, EGFR, PDGFRA/B, ERBB2 and FGFR3 were detected in both cohorts. CONCLUSION Here, we report the molecular aberrations from the largest cohort of patients with mesothelioma. This analysis identified a proportion of patients with targetable alterations and suggests that molecular profiling can identify new treatment options for patients with mesothelioma

Results of variety trials with buckwheat in Switzerland

Выращивание гречихи (Fagopyrum esculentum Moench) имело давнюю традицию в Швейцарии, которая исчезла в XX веке. В течение нескольких последних лет интерес к гречихе вновь возрос, и среди прочего, необходимо было найти сорта, адаптированные к климатическим условиям страны. Поэтому в 2014 году швейцарская сельскохозяйственная научно-исследовательская станция Agroscope начала полевые испытания с различными сортами гречихи. Среди тестируемых сортов было пять с детерминантным типом роста российской селекции из ФГБНУ ВНИИЗБК. Испытания 14 сортов гречихи были проведены в двух точках (Цюрих и Цолликофен) в 2016 году. Урожайность зерна колебалась от 1,57 т/га (Drollet) до 3,38 т/га (Дружина). Влажность зерна при уборке урожая у российских сортов варьировала от 13,6% до 18% в Цюрихе и от 27% до 29,1% в Цолликофене. Возможность с помощью новых сортов гречихи начать успешное производство швейцарских продуктов из гречихи зависит от потребителя, а также от возможностей переработки зерна гречихи (то есть обрушивания) и разработки других продуктов из гречихи кроме муки.Growing buckwheat (Fagopyrum esculentum Moench) had a long tradition in Switzerland which disappeared in the 20th century. Since a few years interest in buckwheat increased again and among others also varieties adapted to the climatic conditions had to be found. Therefore Agroscope, the Swiss Agricultural Research station, initiated field trials with different buckwheat varieties in 2014. Among the tested varieties there were also five with a determinate growth from a Russian breeding program. Trials at two sites (Zurich and Zollikofen) with 14 varieties have been conducted in 2016. Grain yields varied from 15.7 dt/ha (Drollet) up to 33.8 dt/ha (Drushina). The water content of the Russian varieties at harvest varied between 13.6 % and 18 % at Zurich and 27 % and 29.1 % at Zollikofen. In order to confirm results, trials should be repeated again in 2017. Whether with new buckwheat varieties a successful Swiss buckwheat production can be initiated depends on one side on the consumer but also on possibilities of the processing of buckwheat grains (i.e. dehulling) and the development of other buckwheat products than flour

Improving the turnaround time of molecular profiling for advanced non-small cell lung cancer: Outcome of a new algorithm integrating multiple approaches

BACKGROUND Molecular tumor profiling to identify oncogenic drivers and actionable mutations has a profound impact on how lung cancer is treated. Especially in the subgroup of non-small cell lung cancer (NSCLC), molecular testing for certain mutations is crucial in daily clinical practice and is recommended by international guidelines. To date, a standardized approach to identify druggable genetic alterations are lacking. We have developed and implemented a new diagnostic algorithm to harmonize the molecular testing of NSCLC. PATIENTS AND METHODS In this retrospective analysis, we reviewed 119 patients diagnosed with NSCLC at the University Hospital Zurich. Tumor samples were analyzed using our standardized diagnostic algorithm: After the histological diagnosis was made, tissue samples were further analyzed by immunohistochemical stainings as well as the real-time PCR test Idylla™. Extracted DNA was further utilized for comprehensive genomic profiling (FoundationOne®CDx, F1CDx). RESULTS Out of the 119 patients were included in this study, 100 patients were diagnosed with non-squamous NSCLC (nsqNSCLC) and 19 with squamous NSCLC (sqNSCLC). The samples from the nsqNSCLC patients underwent testing by Idylla™ and were evaluated by immunohistochemistry (IHC). F1CDx analysis was run on 67 samples and 46 potentially actionable genomic alterations were detected. Ten patients received the indicated targeted treatment. The median time to test results was 4 days for the Idylla test, 5 days for IHC and 13 days for the F1CDx. CONCLUSION In patients with NSCLC, the implementation of a standardized molecular testing algorithm provided information on predictive markers for NSCLC within a few working days. The implementation of broader genomic profiling led to the identification of actionable targets, which would otherwise not have been discovered

Buchweizenanbau in der Schweiz: neue Sorten für eine alte Nischenkultur

Die Geschichte des Buchweizens reicht weit in die Vergangenheit zurück. Ursprünglich stammt Buchweizen aus China wo Buchweizenarten gemäss Pollenuntersuchungen bereits 2500 v. Chr. wuchsen (Zeller und Hsam 2004). Von dort breitete sich der Buchweizen vermutlich im Mittelalter über Kirgistan, Tadschikistan und Usbekistan in Richtung Europa aus (Zeller 2001). Mit der Intensivierung des Ackerbaus verlor er aber nach und nach an Bedeutung. Aktuell (Datengrundlage 2017) gilt Russland mit 1,52 Millionen Tonnen (von weltweit ca. 4 Millionen Tonnen) als führender Buchweizenproduzent (FAO 2019). In der russischen Küche ist Buchweizen – als Beilage oder Hauptgericht – auch heute noch ein wichtiger Nahrungsbestandteil (Miedaner und Longin 2012). Ab 1400 n. Chr. hat sich der Buchweizenanbau auch in der Schweiz etabliert. Bereits um 1800 n. Chr. beschränkten sich die Anbaugebiete aber nur noch auf einige Täler in Graubünden und im Tessin. (Schilperoord 2017). Hauptgrund war die verstärkte Verbreitung und Förderung des Kartoffelanbaus, was die gesamtschweizerische Anbaufläche von Buchweizen bis ins Jahr 1972 auf unter eine Hektare schrumpfen liess (Lustenberger et al. 1977). Seither taucht Buchweizen nicht mehr einzeln in der Anbaustatistik auf und bis auf die Sorte Brusio ist keine Schweizer Buchweizensorte in der Genbank eingelagert worden (BLW 2019). Seit einigen Jahren nimmt die Bedeutung von Buchweizen in der menschlichen Ernährung aber wieder zu. Gerade für Menschen mit einer Glutenunverträglichkeit (Zöliakie) bietet der glutenfreie Buchweizen eine Alternative zu herkömmlichen Getreideprodukten. Daneben ist Buchweizen auch reich an Spurenelementen wie Zink oder Mangan und wirkt Erkrankungen wie Bluthochdruck oder hohen Cholesterinwerten entgegen (Skrabanja et al. 2004). Aufgrund der geringen Ansprüche an Klima und Boden (Lustenberger et al. 1977) und der eher kurzen Vegetationsdauer von ca. 115 Tagen (Aufhammer et al. 1995) kann Buchweizen als Fruchtfolgeglied interessant sein. Da Buchweizen botanisch gesehen mit keiner anderen häufig in der Schweiz angebauten Kulturpflanze verwandt ist, kann er zur Auflockerung der Fruchtfolge und Aufwertung des Bodens genutzt werden. Durch die kurze Vegetationsdauer besteht zudem die Möglichkeit, Buchweizen als Zweitkultur z. B. nach Wintergerste anzubauen. Als Gründüngungs- und Untersaatenkomponente wird Buchweizen seit vielen Jahren eingesetzt. Unter guten Wachstumsbedingungen ist Buchweizen aufgrund der schnellen Jugendentwicklung ein guter Unkrautunterdrücker. Auch für Insekten ist die Ackerfrucht von Bedeutung, denn sie blüht – je nach Saatzeitpunkt und Sorte – über eine längere Zeit und v. a. während der tendenziell eher trachtarmen Sommermonate. Beim Anbau von Buchweizen als Reinkultur zur Körnernutzung stellen sich zahlreiche Herausforderungen. So ist z. B. die Bestimmung des richtigen Erntezeitpunkts aufgrund des unbegrenzten Wuchses der aktuell verfügbaren Sorten und deshalb auch die Ernte mit dem Mähdrescher schwierig. Neue Züchtungen aus Russland versprechen jedoch eine gleichmässige Abreife bei gleichzeitig hohen Kornerträgen und tieferen Erntefeuchtigkeiten. Um Lösungsansätze für den Buchweizenanbau in der Schweiz zu entwickeln, wurden in einem gemeinsamen Projekt von Agroscope und der Hochschule für Agrar-, Forst- und Lebensmittelwissenschaften HAFL Versuche mit verschiedenen Buchweizensorten und Saatdichten durchgeführt. In den Sortenversuchen wurde zudem der Wert für Bestäuber quantifiziert

FHY1 Mediates Nuclear Import of the Light-Activated Phytochrome A Photoreceptor

The phytochrome (phy) family of photoreceptors is of crucial importance throughout the life cycle of higher plants. Light-induced nuclear import is required for most phytochrome responses. Nuclear accumulation of phyA is dependent on two related proteins called FHY1 (Far-red elongated HYpocotyl 1) and FHL (FHY1 Like), with FHY1 playing the predominant function. The transcription of FHY1 and FHL are controlled by FHY3 (Far-red elongated HYpocotyl 3) and FAR1 (FAr-red impaired Response 1), a related pair of transcription factors, which thus indirectly control phyA nuclear accumulation. FHY1 and FHL preferentially interact with the light-activated form of phyA, but the mechanism by which they enable photoreceptor accumulation in the nucleus remains unsolved. Sequence comparison of numerous FHY1-related proteins indicates that only the NLS located at the N-terminus and the phyA-interaction domain located at the C-terminus are conserved. We demonstrate that these two parts of FHY1 are sufficient for FHY1 function. phyA nuclear accumulation is inhibited in the presence of high levels of FHY1 variants unable to enter the nucleus. Furthermore, nuclear accumulation of phyA becomes light- and FHY1-independent when an NLS sequence is fused to phyA, strongly suggesting that FHY1 mediates nuclear import of light-activated phyA. In accordance with this idea, FHY1 and FHY3 become functionally dispensable in seedlings expressing a constitutively nuclear version of phyA. Our data suggest that the mechanism uncovered in Arabidopsis is conserved in higher plants. Moreover, this mechanism allows us to propose a model explaining why phyA needs a specific nuclear import pathway

Population genomics provide insights into the global genetic structure of Colletotrichum graminicola, the causal agent of maize anthracnose

Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure

Population Genomics Provide Insights into the Global Genetic Structure of \u3ci\u3eColletotrichum graminicola\u3c/i\u3e, the Causal Agent of Maize Anthracnose

Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and wholegenome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure

Characterization of photomorphogenic responses and signaling cascades controlled by phytochrome-A expressed in different tissues:Photomorphogenesis in far-red light

The photoreceptor phytochrome A acts as a light-dependent molecular switch and regulates responses initiated by very low fluences of light (VLFR) and high fluences (HIR) of far-red light. PhyA is expressed ubiquitously, but how phyA signaling is orchestrated to regulate photomorphogenesis is poorly understood. To address this issue, we generated transgenic Arabidopsis thaliana phyA-201 mutant lines expressing the biologically active phyA-YFP photoreceptor in different tissues, and analyzed the expression of several reporter genes, including ProHY5:HY5-GFP and Pro35S:CFP-PIF1, and various FR-HIR-dependent physiological responses. We show that phyA action in one tissue is critical and sufficient to regulate flowering time and root growth; control of cotyledon and hypocotyl growth requires simultaneous phyA activity in different tissues; and changes detected in the expression of reporters are not restricted to phyA-containing cells. We conclude that FR-HIR-controlled morphogenesis in Arabidopsis is mediated partly by tissue-specific and partly by intercellular signaling initiated by phyA. Intercellular signaling is critical for many FR-HIR induced responses, yet it appears that phyA modulates the abundance and activity of key regulatory transcription factors in a tissue-autonomous fashion