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The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions, using signals from nanopore direct RNA sequencing. CHEUI processes observed and expected signals with convolutional neural networks to achieve high single-molecule accuracy and outperform other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI’s capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.
Taphonomy and palaeoecology of Laetoli as well as Makuyuni, Arusha region in northern Tanzania
(2004)
This thesis is the result of the Hominid Corridor research Project in Tanzania since 1993 to 1995 that include Pliocene and Pleistocene localities. The localities under study include Laetoli and Manyara area in Arusha Region, northern Tanzania. The thesis has the following specific objectives: firstly, to identify taxa recovered from the studied assemblages; secondly, to underpin taphonomic history of the assemblages under study; thirdly, to elucidate further palaeoecological reconstruction of the assemblages; and finally, to examine surface fossil fauna modifications including agents of modifications either hominids or carnivores.
The Upper Laetolil Beds are dated at 3.5 million years ago (Ma) and the Ndolanya Beds are bracketed in age between 3.5 and 2.41 Ma. The Naibadad Beds, also from Laetoli area, are date to be between 2.2 to 2.1 Ma. The Naibadad Beds are correlated with the base of Bed I at Olduvai Gorge. There are so far no absolute dates for Manyara assemblages. Based on biostratigraphic correlation, the younger overlying unit, the Upper Manyara Beds are estimated to belong to Later Pleistocene and the Lower Manyara Beds are estimated to belong to Early Pleistocene. The Upper Manyara Beds are correlated to the age of Bed III at Olduvai Gorge, while the Lower Manyara Beds are interpreted to span the same contemporaneity with the upper part of Bed II at Olduvai Gorge.
At Laetoli localities, terrestrial mammals while localities from Manyara besides terrestrial mammals dominate fauna; they include aquatic species such as fish, crocodiles and hippopotamus. The main families recovered from Upper Laetolil Beds complement those already recovered from former research works by other workers. This is also true for the younger overlying stratigraphic horizon, the Upper Ndolanya Beds. Thus, mammalian families recovered from Upper Laetolil Beds include Bovidae, Carnivora, Elephantidae, Equidae, Lagomorpha, Suidae, Rodentia, Hominoidea and Rhenocerotidae. Remains of an invertebrate, Gastropoda were also recovered. For Upper Ndolanya Beds include almost the same families recovered from Upper Laetolil Beds, but based on former recovery of fossil fauna, these Beds outnumber greatly the Upper Laetolil Beds in bovid composition by 20 per cent. Such a change in species composition is noticed also from South African localities and East African localities such as the East Turkana. This is interpreted to be due to climatic change drier environments that included species adapted to such palaeoclimates.
For the first time, our team has been able to retrieve specimens identifiable to taxa, a pattern that not possible from previous workers who claimed to have recovered too sparse specimens to be identifiable to any taxon.
The Upper Manyara Beds as well as Lower Manyara taxonomic composition include aquatic species besides the large terrestrial mammalian fauna retrieved from there. In due regard, the former horizon is attributed to have affinity with Olduvai Bed III components and the latter, older horizon, is attributed to have affinity with upper parts of Bed II times at Olduvai Gorge. The Lower Manyara Beds can be said to have, in relative terms, affinity to species recovered from site RC 11 of the Chiwondo Beds, Malema region in northern Malawi, although the former site may be equable to the terminal age of the latter locality.
Fossil hominid remains; attributable to genus Homo and possibly species Homo erectus have been recovered from two localities, Mk 2 and Mk, along Lower Manyara Beds. On the other hand, stone tools, identified to belong to the Acheulian industrial technocomplex, were recovered from site Mk 4.
All of fossil fauna from Laetoli sites were mostly exfoliated and there shows to be little effect in terms of hydrodynamic sorting of the fossil bones. However, intense carnivore activity is witnessed due to the almost one to one ratio of proximal to distal ends. This is also true for the Lower Manyara Beds locality. Through examination of surface modifications of the fossil fauna, it has been established that there was carnivore consumption of ungulates. There is no evidence of hominid involvement that has to be testified by stone tools.
Tree-related microhabitats (TreMs) describe the microhabitats that a tree can provide for a multitude of other taxonomic groups and have been proposed as an important indicator for forest biodiversity (Asbeck et al., 2021). So far, the focus of TreM studies has been on temperate forests, although many trees in the tropics harbour exceptionally high numbers of TreMs. In this study, TreMs in the lowland tropical forests of the Choco (Ecuador) and in the mountain tropical forests of Mount Kilimanjaro (Tanzania) were surveyed. Our results extend the existing typology of TreMs of Larrieu et al. (2018) to include tropical forests and enabled a comparison of the relative recordings and diversity of TreMs between tropical and temperate forests. A new TreM form, Root formations, and three new TreM groups, concavities build by fruits or leaves, dendrotelms, and root formations, were established. In total, 15 new TreM types in five different TreM groups were specified. The relative recordings of most TreMs were similar between tropical and temperate forests. However, ivy and lianas, and ferns were more common in the lowland rainforest than in temperate forests, and bark microsoil, limb breakage, and foliose and fruticose lichens in tropical montane forest than in lowland rainforest. Mountain tropical forests hosted the highest diversity for common and dominant TreM types, and lowland tropical forest the highest diversity for rare TreMs. Our extended typology of tree-related microhabitats can support studies of forest-dwelling biodiversity in tropical forests. Specifically, given the ongoing threat to tropical forests, TreMs can serve as an additional tool allowing rapid assessments of biodiversity in these hyperdiverse ecosystems.
Die Transkription vieler Gene wird über den Acetylierungsgrad der Histone reguliert. Entsprechend erweiterte die Entdeckung von Histondeacetylase-Inhibitoren das Verständnis um Transkriptions-Repressoren und ihre Rolle in der Pathogenese beträchtlich. Zur Zeit stehen die Modifikationen der Histondeacetylasen (HDACs) sowie die biologischen Rollen der verschiedenen HDAC-Isoenzyme im Zentrum intensiver Forschungsarbeiten.
In der vorliegenden Arbeit wurde anhand verschiedener Zelllinien und mit murinem Primärmaterial nachgewiesen, dass das gut verträgliche Antiepileptikum Valproinsäure (VPA) ein potenter HDAC-Inhibitor ist. Dies zeigt sich daran, dass VPA in vivo die durch HDACs vermittelte transkriptionelle Repression aufhebt und zur Akkumulation hyperacetylierter Histone führt. In vitro Enzymassays weisen darauf hin, dass VPA selbst und nicht ein hypothetischer Metabolit die Histondeacetylasen hemmt. Darüber hinaus wurde mit Bindungs- und Kompetitionsstudien festgestellt, dass eine Interaktion von VPA mit dem katalytischen Zentrum der HDACs stattfindet.
Weitere Analysen zeigten, dass VPA bevorzugt Klasse I HDACs hemmt. Durch dieses Merkmal einer erhöhten Spezifität bei gleichzeitig guter Bioverfügbarkeit definiert VPA eine neue Klasse von HDAC-Inhibitoren. Hieraus ergeben sich Hinweise auf strukturelle Anforderungen, die ein HDAC-Inhibitor erfüllen muß, um spezifischer und weniger toxisch als konventionelle Chemotherapeutika zu wirken. Außerdem eröffnete das neu entdeckte pharmakologische Wirkungsspektrum von VPA auf HDACs Erkenntnisse um zusätzliche therapeutische Einsatzmöglichkeiten dieses etablierten Arzneimittels. Bereits jetzt wird VPA in klinischen Studien an Patienten mit Krebs verabreicht.
HDAC-Inhibitoren gelten als potentielle Medikamente für die Therapie maligner Neoplasien. Deshalb besteht großes Interesse an den molekularen Mechanismen, mit denen Substanzen dieser Wirkstoffklasse das Wachstum transformierter Zellen in vitro und in vivo hemmen. In den humanen Melanomzelllinien SK-Mel-37 und Mz-Mel-19 bewirken klinisch relevante VPA-Dosen eine zeit- und dosisabhängige Akkumulation von Zellzyklusinhibitoren und hyperacetylierten Histonen, morphologische Veränderungen und eine verringerte Proliferationsrate. Die verminderte Proliferation wird von einem veränderten Zellzyklusprofil und Apoptose unter Beteiligung sowohl der extrinsisch als auch der intrinsisch bedingten Caspase-Kaskade begleitet. Dies manifestiert sich in der Spaltung der Caspasen 3, 8 und 9, einer Schädigung der Mitochondrien, der apoptotischen PARP-Spaltung, einem Abbau der genomischen DNA und einer Inaktivierung des GFP-Proteins.
Diese Analysen in Melanomzellen sprechen dafür, dass die weitgehend selektive Wirkung von VPA auf Klasse I HDACs der Mechanismus ist, mit dem diese Substanz das Wachstum bestimmter Tumorzellen hemmt. Durch Genexpressions-Analysen konnten außerdem neue Modelle zum Einfluss von VPA auf solide Tumoren postuliert werden. Darüber hinaus wurde festgestellt, dass die Expression und Induzierbarkeit der Zellzyklusregulatoren p21WAF/CIP1 und p27Kip1 und des latent cytoplasmatischen Transkriptionsfaktors Stat1 Biomarker für die Sensitivität von Melanomzellen gegenüber HDAC-Inhibitoren sind. Im Einklang hiermit wird die proapoptotische Wirkung von VPA durch das Cytokin Interferon α und den S-Phase-Inhibitor Hydroxyharnstoff deutlich gesteigert. Diese Ergebnisse sprechen für den Einsatz von VPA in tierexperimentellen und klinischen Studien.
Aufgrund der Schlüsselrolle der HDACs für die physiologische und aberrante Genexpression ist es wichtig, die Mechanismen ihrer Regulation zu kennen. In der vorliegenden Arbeit wurde anhand zahlreicher kultivierter Zelllinien und mittels eines Mausmodells gezeigt, dass therapeutisch einsetzbare VPA-Dosen neben der Hemmung enzymatischer Aktivität auch zu einer isoenzymspezifischen Verringerung der Klasse I Histondeacetylase HDAC2 führen. Als Ursache hierfür konnten eine verstärkte Poly-Ubiquitinylierung und ein proteasomaler Abbau ermittelt werden. Gleichzeitig wurden die Beteiligung etlicher Proteasen und eine veränderte Synthese oder Prozessierung der HDAC2-mRNA als Mechanismen ausgeschlossen.
Expressionsanalysen identifizierten die E2 Ubiquitinkonjugase Ubc8 als von HDAC-Inhibitoren induziertes Gen. Mittels transienter Überexpression („Gain-of-Function“) und siRNA-Experimenten („Loss-of-Function“) konnte dieses Gen als limitierender Faktor des HDAC2-Umsatzes in vivo erkannt werden. Weiterhin wurde gezeigt, dass die E3 Ubiquitinligase RLIM spezifisch mit HDAC2 interagiert. Die Expression von RLIM beziehungsweise seine enzymatische Funktion beeinflusst die HDAC2-Konzentration in vivo. Hierbei kann VPA klar von dem HDACInhibitor Trichostatin A (TSA) abgegrenzt werden. Dieser hemmt ein breites Spektrum an HDACs und induziert Ubc8, führt aber gleichzeitig zu einem proteasomal vermittelten Abbau des RLIM-Proteins. Analysen mit überexprimiertem RLIM zeigten, dass TSA aufgrund dieses Mechanismus nicht in der Lage ist, den Abbau von HDAC2 zu induzieren. Somit ist im Rahmen dieser Arbeit die Ubiquitinylierungs-Maschinerie für HDAC2 charakterisiert worden. Hierdurch sind neue Aspekte zum Zusammenspiel zwischen dem Ubiquitin-Proteasom-System und der Transkriptionsrepression nachgewiesen worden.
Isoenzymspezifische HDAC-Inhibitoren können zur Aufklärung der Funktion einzelner Histondeacetylasen beitragen, insbesondere wenn Knock-Out-Studien zu aufwendig oder aufgrund embryonaler Letalität nicht durchführbar sind. Die Wichtigkeit dieser Analysen wird gerade bei HDAC2 deutlich, da diese Histondeacetylase in vielen soliden und hämatologischen Tumoren überexprimiert ist, und ihre Deregulation möglicherweise zur Krebsentstehung beiträgt. Die in der vorliegenden Arbeit identifizierte Regulation dieses HDAC-Isoenzyms könnte Hinweise auf den Ablauf eines malignen Transformationsprozesses geben. Darüber hinaus zeigt der nachgewiesene Regulationsmechanismus Erfordernisse und potentielle Zielstrukturen einer pharmakologischen Intervention auf. Schließlich könnten die Selektivität von VPA für Klasse I HDACs zusammen mit der Spezifität für HDAC2 die Gründe für die geringen Nebenwirkungen der VPA-Behandlung bei gleichzeitigem Auftreten antitumoraler Effekte sein.
In high light, the antenna system in oxygenic photosynthetic organisms switches to a photoprotective mode, dissipating excess energy in a process called non-photochemical quenching (NPQ). Diatoms exhibit very efficient NPQ, accompanied by a xanthophyll cycle in which diadinoxanthin is de-epoxidized into diatoxanthin. Diatoms accumulate pigments from this cycle in high light, and exhibit faster and more pronounced NPQ. The mechanisms underlying NPQ in diatoms remain unclear, but it can be mimicked by aggregation of their isolated light-harvesting complexes, FCP (fucoxanthin chlorophyll-a/c protein). We assess this model system by resonance Raman measurements of two peripheral FCPs, trimeric FCPa and nonameric FCPb, isolated from high- and low-light-adapted cells (LL, HL). Quenching is associated with a reorganisation of these proteins, affecting the conformation of their bound carotenoids, and in a manner which is highly dependent on the protein considered. FCPa from LL diatoms exhibits significant changes in diadinoxanthin structure, together with a smaller conformational change of at least one fucoxanthin. For these LL-FCPa, quenching is associated with consecutive events, displaying distinct spectral signatures, and its amplitude correlates with the planarity of the diadinoxanthin structure. HL-FCPa aggregation is associated with a change in planarity of a 515-nm-absorbing fucoxanthin, and, to a lesser extent, of diadinoxanthin. Finally, in FCPb, a blue-absorbing fucoxanthin is primarily affected. FCPs thus possess a plastic structure, undergoing several conformational changes upon aggregation, dependent upon their precise composition and structure. NPQ in diatoms may therefore arise from a combination of structural changes, dependent on the environment the cells are adapted to.
Abstract
Natural plant populations often harbour substantial heritable variation in DNA methylation. However, a thorough understanding of the genetic and environmental drivers of this epigenetic variation requires large-scale and high-resolution data, which currently exist only for a few model species. Here, we studied 207 lines of the annual weed Thlaspi arvense (field pennycress), collected across a large latitudinal gradient in Europe and propagated in a common environment. By screening for variation in DNA sequence and DNA methylation using whole-genome (bisulfite) sequencing, we found significant epigenetic population structure across Europe. Average levels of DNA methylation were strongly context-dependent, with highest DNA methylation in CG context, particularly in transposable elements and in intergenic regions. Residual DNA methylation variation within all contexts was associated with genetic variants, which often co-localized with annotated methylation machinery genes but also with new candidates. Variation in DNA methylation was also significantly associated with climate of origin, with methylation levels being higher in warmer regions and lower in more variable climates. Finally, we used variance decomposition to assess genetic versus environmental associations with differentially methylation regions (DMRs). We found that while genetic variation was generally the strongest predictor of DMRs, the strength of environmental associations increased from CG to CHG and CHH, with climate-of-origin as the strongest predictor in about one third of the CHH DMRs. In summary, our data show that natural epigenetic variation in Thlaspi arvense is significantly associated with both DNA sequence and environment of origin, and that the relative importance of the two factors strongly depends on the sequence context of DNA methylation. T. arvense is an emerging biofuel and winter cover crop; our results may hence be relevant for breeding efforts and agricultural practices in the context of rapidly changing environmental conditions.
Author Summary: Variation within species is an important level of biodiversity, and it is key for future adaptation. Besides variation in DNA sequence, plants also harbour heritable variation in DNA methylation, and we want to understand the evolutionary significance of this epigenetic variation, in particular how much of it is under genetic control, and how much is associated with the environment. We addressed these questions in a high-resolution molecular analysis of 207 lines of the common plant field pennycress (Thlaspi arvense), which we collected across Europe, propagated under standardized conditions, and sequenced for their genetic and epigenetic variation. We found large geographic variation in DNA methylation, associated with both DNA sequence and climate of origin. Genetic variation was generally the stronger predictor of DNA methylation variation, but the strength of environmental association varied between different sequence contexts. Climate-of-origin was the strongest predictor in about one third of the differentially methylated regions in the CHH context, which suggests that epigenetic variation may play a role in the short-term climate adaptation of pennycress. As pennycress is currently being domesticated as a new biofuel and winter cover crop, our results may be relevant also for agriculture, particularly in changing environments.
Meliolales (black mildews) is an order of plant parasitic ascomycetous fungi in the tropics and subtropics. They are frequently overgrown and parasitized by other fungi, known as hyperparasites. During the last few years, species of hyperparasitic fungi on Meliolales have been collected in Benin and Panama. A new species of Paranectria and seven new reports of hyperparasites of different systematic groups are presented here with detailed descriptions and illustrations, together with new data concerning fungal hosts and host plants. The new species is called Paranectria longiappendiculata, characterized by exceptionally long appendages carried by the ascospores. New records for Benin and Panama are Calloriopsis herpotricha, Dimerosporiella cephalosporii, Isthmospora glabra, Isthmospora trichophila, Malacaria meliolicola, Paranectriella hemileiae, and Paranectriella minuta. Calloriopsis herpotricha is recorded for Africa and D. cephalosporii and P. hemileiae for America for the first time, suggesting an apparently pantropical distribution. Findings show a blatant lack of investigation on hyperparasitic fungi in the tropics. The phylogenetic positions of three of these newly reported species, C. herpotricha, D. cephalosporii, and P. minuta, are shown based on the analysis of internal transcribed spacer (ITS), large subunit (LSU), and small subunit (SSU) rDNA sequences. These sequences were generated in the context of the present study for the first time.