Tibetan terrestrial and aquatic ecosystems collapsed with cryosphere loss inferred from sedimentary ancient metagenomics.

Glacier and permafrost shrinkage and land-use intensification threaten mountain wildlife and affect nature conservation strategies. Here, we present paleometagenomic records of terrestrial and aquatic taxa from the southeastern Tibetan Plateau covering the last 18,000 years to help understand the complex alpine ecosystem dynamics. We infer that steppe-meadow became woodland at 14 ka (cal BP) controlled by cryosphere loss, further driving a herbivore change from wild yak to deer. These findings weaken the hypothesis of top-down control by large herbivores in the terrestrial ecosystem. We find a turnover in the aquatic communities at 14 ka, transitioning from glacier-related (blue-green) algae to abundant nonglacier-preferring picocyanobacteria, macrophytes, fish, and otters. There is no evidence for substantial effects of livestock herding in either ecosystem. Using network analysis, we assess the stress-gradient hypothesis and reveal that root hemiparasitic and cushion plants are keystone taxa. With ongoing cryosphere loss, the protection of their habitats is likely to be of conservation benefit on the Tibetan Plateau.

Simulating long-term wildfire impacts on boreal forest structure in Central Yakutia, Siberia, since the Last Glacial Maximum.

Background: Wildfires are recognized as an important ecological component of larch-dominated boreal forests in eastern Siberia. However, long-term fire-vegetation dynamics in this unique environment are poorly understood. Recent paleoecological research suggests that intensifying fire regimes may induce millennial-scale shifts in forest structure and composition. This may, in turn, result in positive feedback on intensifying wildfires and permafrost degradation, apart from threatening human livelihoods. Most common fire-vegetation models do not explicitly include detailed individual-based tree population dynamics, but a focus on patterns of forest structure emerging from interactions among individual trees may provide a beneficial perspective on the impacts of changing fire regimes in eastern Siberia. To simulate these impacts on forest structure at millennial timescales, we apply the individual-based, spatially explicit vegetation model LAVESI-FIRE, expanded with a new fire module. Satellite-based fire observations along with fieldwork data were used to inform the implementation of wildfire occurrence and adjust model parameters. Results: Simulations of annual forest development and wildfire activity at a study site in the Republic of Sakha (Yakutia) since the Last Glacial Maximum (c. 20,000 years BP) highlight the variable impacts of fire regimes on forest structure throughout time. Modeled annual fire probability and subsequent burned area in the Holocene compare well with a local reconstruction of charcoal influx in lake sediments. Wildfires can be followed by different forest regeneration pathways, depending on fire frequency and intensity and the pre-fire forest conditions. We find that medium-intensity wildfires at fire return intervals of 50 years or more benefit the dominance of fire-resisting Dahurian larch (Larix gmelinii (Rupr.) Rupr.), while stand-replacing fires tend to enable the establishment of evergreen conifers. Apart from post-fire mortality, wildfires modulate forest development mainly through competition effects and a reduction of the model's litter layer. Conclusion: With its fine-scale population dynamics, LAVESI-FIRE can serve as a highly localized, spatially explicit tool to understand the long-term impacts of boreal wildfires on forest structure and to better constrain interpretations of paleoecological reconstructions of fire activity. Supplementary Information: The online version contains supplementary material available at 10.1186/s42408-023-00238-8.

Antecedentes: Los incendios de vegetación son reconocidos como un componente importante de los bosques boreales dominados por alerces en el este de Siberia. Sin embargo, la dinámica a largo plazo entre fuegos y vegetación en este ambiente único es pobremente entendido. Estudios paleo-ecológicos recientes sugieren que la intensificación de regímenes de fuego puede inducir cambios, a escala de milenos, en la estructura y composición de estos bosques. Estos pueden, a su vez, resultar en una retroalimentación positiva en la intensificación de los incendios y en la degradación del permafrost, aparte de amenazar la vida humana. Los modelos de fuego-vegetación más comunes, no incluyen específicamente detalles basados en la dinámica poblacional de árboles individuales, aunque el enfocarnos en los patrones de la estructura forestal que emerge de interacciones entre árboles individuales puede proveer de una perspectiva beneficiosa sobre los impactos de los cambios en los regímenes del fuego en el este de Siberia. Para simular estos impactos en la estructura forestal a escalas de milenios, aplicamos el modelo espacialmente explícito, individualmente basado, LAVESI-FIRE, expandido en un nuevo módulo de fuego. Observaciones de fuego basadas en imágenes satelitales junto con datos de campo fueron usados para informar la implementación de la ocurrencia de fuegos de vegetación y ajustar los parámetros del modelo. Resultados: Las simulaciones del desarrollo anual de los bosques y de la actividad de los incendios en un sitio de estudio de la República de Sakha (Yakutia) desde el Último Máximo Glacial (c. 20.000 años atrás), resaltan los impactos variables de los regímenes de fuegos en la estructura forestal a través del tiempo. La probabilidad modelada de forma anual en la ocurrencia de incendios y subsecuentemente del área quemada durante el Holoceno se compara muy bien con la reconstrucción del flujo de carbón en los sedimentos lacustres. Los incendios de vegetación pueden verse mediante diferentes patrones de regeneración del bosque, dependiendo de la frecuencia e intensidad de los fuegos y de las condiciones del bosque en el pre-fuego. Encontramos que fuegos de mediana intensidad a intervalos de retorno de unos 50 años o más, benefician la persistencia del alerce dahurian (Larix gmelinii (Rupr.) Rupr.), especie resistente al fuego, mientras que los fuegos de reemplazo tienden a permitir el establecimiento de coníferas siempreverdes. Aparte de la mortalidad post-fuego, los fuegos de vegetación modulan el desarrollo del bosque, fundamentalmente a través de efectos de competencia y una reducción de la capa de mantillo predicho por el modelo. Conclusiones: Con sus características de detectar la dinámica de la población a una escala fina, el modelo LAVESI-FIRE puede servir como una herramienta altamente localizada y espacialmente explícita, para entender los impactos a largo plazo de los bosques boreales sobre la estructura forestal y para mejorar los condicionamientos de las interpretaciones de las reconstrucciones paleo ecológicas en la reconstrucción de la actividad de los incendios.

Evolutionary adaptation of trees and modelled future larch forest extent in Siberia.

With changing climate, the boreal forest could potentially migrate north and become threatened by droughts in the south. However, whether larches, the dominant tree species in eastern Siberia, can adapt to novel situations is largely unknown but is crucial for predicting future population dynamics. Exploring variable traits and trait adaptation through inheritance in an individual-based model can improve our understanding and help future projections. We updated the individual-based spatially explicit vegetation model LAVESI (Larix Vegetation Simulator), used for forest predictions in Eastern Siberia, with trait value variation and incorporated inheritance of parental values to their offspring. Forcing the model with both past and future climate projections, we simulated two areas - the expanding northern treeline and a southerly area experiencing drought. While the specific trait of 'seed weight' regulates migration, the abstract 'drought resistance' protects stands. We show that trait variation with inheritance leads to an increase in migration rate (∼ 3% area increase until 2100). The drought resistance simulations show that, under increasing stress, including adaptive traits leads to larger surviving populations (17% of threatened under RCP 4.5 (Representative Concentration Pathway)). We show that with the increase expected under the RCP 8.5 scenario vast areas (80% of the extrapolated area) of larch forest are threatened and could disappear due to drought as adaptation plays only a minor role under strong warming. We conclude that variable traits facilitate the availability of variants under environmental changes. Inheritance allows populations to adapt to environments and promote successful traits, which leads to populations that can spread faster and be more resilient, provided the changes are not too drastic in both time and magnitude. We show that trait variation and inheritance contribute to more accurate models that can improve our understanding of responses of boreal forests to global change.

Regional opportunities for tundra conservation in the next 1000 years.

The biodiversity of tundra areas in northern high latitudes is threatened by invasion of forests under global warming. However, poorly understood nonlinear responses of the treeline ecotone mean the timing and extent of tundra losses are unclear, but policymakers need such information to optimize conservation efforts. Our individual-based model LAVESI, developed for the Siberian tundra-taiga ecotone, can help improve our understanding. Consequently, we simulated treeline migration trajectories until the end of the millennium, causing a loss of tundra area when advancing north. Our simulations reveal that the treeline follows climate warming with a severe, century-long time lag, which is overcompensated by infilling of stands in the long run even when temperatures cool again. Our simulations reveal that only under ambitious mitigation strategies (relative concentration pathway 2.6) will ∼30% of original tundra areas remain in the north but separated into two disjunct refugia.

Sedimentary ancient DNA reveals a threat of warming-induced alpine habitat loss to Tibetan Plateau plant diversity.

Studies along elevational gradients worldwide usually find the highest plant taxa richness in mid-elevation forest belts. Hence, an increase in upper elevation diversity is expected in the course of warming-related treeline rise. Here, we use a time-series approach to infer past taxa richness from sedimentary ancient DNA from the south-eastern Tibetan Plateau over the last ~18,000 years. We find the highest total plant taxa richness during the cool phase after glacier retreat when the area contained extensive and diverse alpine habitats (14-10 ka); followed by a decline when forests expanded during the warm early- to mid-Holocene (10-3.6 ka). Livestock grazing since 3.6 ka promoted plant taxa richness only weakly. Based on these inferred dependencies, our simulation yields a substantive decrease in plant taxa richness in response to warming-related alpine habitat loss over the next centuries. Accordingly, efforts of Tibetan biodiversity conservation should include conclusions from palaeoecological evidence.

Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene.

Microbial communities involving dehalogenating bacteria assist in bioremediation of areas contaminated with halocarbons. To understand molecular interactions between dehalogenating bacteria, we co-cultured Sulfurospirillum multivorans, dechlorinating tetrachloroethene (PCE) to cis-1,2-dichloroethene (cDCE), and Dehalococcoides mccartyi strains BTF08 or 195, dehalogenating PCE to ethene. The co-cultures were cultivated with lactate as electron donor. In co-cultures, the bacterial cells formed aggregates and D. mccartyi established an unusual, barrel-like morphology. An extracellular matrix surrounding bacterial cells in the aggregates enhanced cell-to-cell contact. PCE was dehalogenated to ethene at least three times faster in the co-culture. The dehalogenation was carried out via PceA of S. multivorans, and PteA (a recently described PCE dehalogenase) and VcrA of D. mccartyi BTF08, as supported by protein abundance. The co-culture was not dependent on exogenous hydrogen and acetate, suggesting a syntrophic relationship in which the obligate hydrogen consumer D. mccartyi consumes hydrogen and acetate produced by S. multivorans. The cobamide cofactor of the reductive dehalogenase-mandatory for D. mccartyi-was also produced by S. multivorans. D. mccartyi strain 195 dechlorinated cDCE in the presence of norpseudo-B12 produced by S. multivorans, but D. mccartyi strain BTF08 depended on an exogenous lower cobamide ligand. This observation is important for bioremediation, since cofactor supply in the environment might be a limiting factor for PCE dehalogenation to ethene, described for D. mccartyi exclusively. The findings from this co-culture give new insights into aggregate formation and the physiology of D. mccartyi within a bacterial community.

[Usability and Efficiency of a Digital Communication Assistance Tool to Obtain Medical History from Non-German-Speaking Patients]. / Nutzbarkeit digitaler Anamnesehilfen für nicht-deutschsprachige Patienten in der allgemeinärztlichen Sprechstunde.

AIM: In the DICTUM-Friedland study, a medical history-taking app was implemented in an initial reception facility for refugees and asylum seekers. This app can be used to obtain from patients information about the most frequent general medical complaints and risk factors in 13 different languages or dialects. A report (synopsis) is generated, based on each patient's given data, in the German language. Usability and efficiency of obtaining medical history were the criteria evaluated in order to test and optimize the app for use in a broader general medical setting. METHODS: From May to December 2018, the app was tested in the waiting room of the general medical ward in the refugee camp in Friedland in southern Lower Saxony, Germany. Patients were asked to complete a short digital questionnaire about the usability of the app immediately after finishing the query. Sociodemographic data were partly collected with the same questionnaire and partly extracted from patient records. The efficiency was evaluated on the basis of the correspondence between the entered complaints (ICPC-2) and the diagnoses of the doctors (ICD-10). RESULTS: In total, the app was used 353 times, and based on these, 283 medical histories were taken. The median time for entering the complaints was 10:27 minutes. The use of the audio output (60% of patients used this option) did not influence the usability. The majority of the users (76%) rated the app as easy to use and 65% of the users stated that they were able to enter their main complaints. Both assessments were independent of the age and sex of the users, but the educational level had a slightly more positive influence. The efficiency test showed that 51% (n=144) of the synopses matched fully and 28% (n=79) of the synopses matched partially with the medical diagnoses. CONCLUSION: The systematic survey of the most frequent general medical complaints enables a more precise medical history taking in patients with whom a normal interview is not possible due to language barriers. Thus it serves as a support for the medical history taking. The app is easy to use and not prone to the errors of online translations.

Long-lived larch clones may conserve adaptations that could restrict treeline migration in northern Siberia.

The occurrence of refugia beyond the arctic treeline and genetic adaptation therein play a crucial role of largely unknown effect size. While refugia have potential for rapidly colonizing the tundra under global warming, the taxa may be maladapted to the new environmental conditions. Understanding the genetic composition and age of refugia is thus crucial for predicting any migration response. Here, we genotype 194 larch individuals from an ~1.8 km2 area in northcentral Siberia on the southern Taimyr Peninsula by applying an assay of 16 nuclear microsatellite markers. For estimating the age of clonal individuals, we counted tree rings at sections along branches to establish a lateral growth rate that was then combined with geographic distance. Findings reveal that the predominant reproduction type is clonal (58.76%) by short distance spreading of ramets. One outlier of clones 1 km apart could have been dispersed by reindeer. In clonal groups and within individuals, we find that somatic mutations accumulate with geographic distance. Clonal groups of two or more individuals are observed. Clonal age estimates regularly suggest individuals as old as 2,200 years, which coincides with a major environmental change that forced a treeline retreat in the region. We conclude that individuals with clonal growth mode were naturally selected as it lowers the likely risk of extinction under a harsh environment. We discuss this legacy from the past that might now be a maladaptation and hinder expansion under currently strongly increasing temperatures.

A Digital Communication Assistance Tool (DCAT) toObtain Medical History from Foreign-LanguagePatients: Development and Pilot Testing in a PrimaryHealth Care Center for Refugees.

BACKGROUND: Language barriers play a critical role in the treatment of migrant and refugeepatients. In Germany, primary care interpreters are often not available especially in rural areas or ifpatients demand spontaneous or urgent consultations. Methods: In order to enable patients and theirphysicians to communicate effectively about the current illness history, we developed a digitalcommunication assistance tool (DCAT) for 19 different languages and dialects. This paper reportsthe multidisciplinary process of the conceptual design and the iterative development of this crossculturaluser-centered application in an action-oriented approach. Results: We piloted our app with36 refugee patients prior to a clinical study and used the results for further development. Theacceptance and usability of the app by patients was high. Conclusion: Using digital tools forovercoming language barriers can be a feasible approach when providing health care to foreignlanguagepatients.

Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly.

Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.

Guided cobamide biosynthesis for heterologous production of reductive dehalogenases.

Cobamides (Cbas) are essential cofactors of reductive dehalogenases (RDases) in organohalide-respiring bacteria (OHRB). Changes in the Cba structure can influence RDase function. Here, we report on the cofactor versatility or selectivity of Desulfitobacterium RDases produced either in the native organism or heterologously. The susceptibility of Desulfitobacterium hafniense strain DCB-2 to guided Cba biosynthesis (i.e. incorporation of exogenous Cba lower ligand base precursors) was analysed. Exogenous benzimidazoles, azabenzimidazoles and 4,5-dimethylimidazole were incorporated by the organism into Cbas. When the type of Cba changed, no effect on the turnover rate of the 3-chloro-4-hydroxy-phenylacetate-converting enzyme RdhA6 and the 3,5-dichlorophenol-dehalogenating enzyme RdhA3 was observed. The impact of the amendment of Cba lower ligand precursors on RDase function was also investigated in Shimwellia blattae, the Cba producer used for the heterologous production of Desulfitobacterium RDases. The recombinant tetrachloroethene RDase (PceAY51 ) appeared to be non-selective towards different Cbas. However, the functional production of the 1,2-dichloroethane-dihaloeliminating enzyme (DcaA) of Desulfitobacterium dichloroeliminans was completely prevented in cells producing 5,6-dimethylbenzimidazolyl-Cba, but substantially enhanced in cells that incorporated 5-methoxybenzimidazole into the Cba cofactor. The results of the study indicate the utilization of a range of different Cbas by Desulfitobacterium RDases with selected representatives apparently preferring distinct Cbas.

Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling.

Changes in species' distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species' range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.

Hydrogen production by Sulfurospirillum species enables syntrophic interactions of Epsilonproteobacteria.

Hydrogen-producing bacteria are of environmental importance, since hydrogen is a major electron donor for prokaryotes in anoxic ecosystems. Epsilonproteobacteria are currently considered to be hydrogen-oxidizing bacteria exclusively. Here, we report hydrogen production upon pyruvate fermentation for free-living Epsilonproteobacteria, Sulfurospirillum spp. The amount of hydrogen produced is different in two subgroups of Sulfurospirillum spp., represented by S. cavolei and S. multivorans. The former produces more hydrogen and excretes acetate as sole organic acid, while the latter additionally produces lactate and succinate. Hydrogen production can be assigned by differential proteomics to a hydrogenase (similar to hydrogenase 4 from E. coli) that is more abundant during fermentation. A syntrophic interaction is established between Sulfurospirillum multivorans and Methanococcus voltae when cocultured with lactate as sole substrate, as the former cannot grow fermentatively on lactate alone and the latter relies on hydrogen for growth. This might hint to a yet unrecognized role of Epsilonproteobacteria as hydrogen producers in anoxic microbial communities.

Dissimilar responses of larch stands in northern Siberia to increasing temperatures-a field and simulation based study.

Arctic and alpine treelines worldwide differ in their reactions to climate change. A northward advance of or densification within the treeline ecotone will likely influence climate-vegetation feedback mechanisms. In our study, which was conducted in the Taimyr Depression in the North Siberian Lowlands, w present a combined field- and model-based approach helping us to better understand the population processes involved in the responses of the whole treeline ecotone, spanning from closed forest to single-tree tundra, to climate warming. Using information on stand structure, tree age, and seed quality and quantity from seven sites, we investigate effects of intra-specific competition and seed availability on the specific impact of recent climate warming on larch stands. Field data show that tree density is highest in the forest-tundra, and average tree size decreases from closed forest to single-tree tundra. Age-structure analyses indicate that the trees in the closed forest and forest-tundra have been present for at least ~240 yr. At all sites except the most southerly ones, past establishment is positively correlated with regional temperature increase. In the single-tree tundra, however, a change in growth form from krummholz to erect trees, beginning ~130 yr ago, rather than establishment date has been recorded. Seed mass decreases from south to north, while seed quantity increases. Simulations with LAVESI (Larix Vegetation Simulator) further suggest that relative density changes strongly in response to a warming signal in the forest-tundra while intra-specific competition limits densification in the closed forest and seed limitation hinders densification in the single-tree tundra. We find striking differences in strength and timing of responses to recent climate warming. While forest-tundra stands recently densified, recruitment is almost non-existent at the southern and northern end of the ecotone due to autecological processes. Palaeo-treelines may therefore be inappropriate to infer past temperature changes at a fine scale. Moreover, a lagged treeline response to past warming will, via feedback mechanisms, influence climate change in the future.

The NiFe Hydrogenases of the Tetrachloroethene-Respiring Epsilonproteobacterium Sulfurospirillum multivorans: Biochemical Studies and Transcription Analysis.

The organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans is able to grow with hydrogen as electron donor and with tetrachloroethene (PCE) as electron acceptor; PCE is reductively dechlorinated to cis-1,2-dichloroethene. Recently, a genomic survey revealed the presence of four gene clusters encoding NiFe hydrogenases in its genome, one of which is presumably periplasmic and membrane-bound (MBH), whereas the remaining three are cytoplasmic. To explore the role and regulation of the four hydrogenases, quantitative real-time PCR and biochemical studies were performed with S. multivorans cells grown under different growth conditions. The large subunit genes of the MBH and of a cytoplasmic group 4 hydrogenase, which is assumed to be membrane-associated, show high transcript levels under nearly all growth conditions tested, pointing toward a constitutive expression in S. multivorans. The gene transcripts encoding the large subunits of the other two hydrogenases were either not detected at all or only present at very low amounts. The presence of MBH under all growth conditions tested, even with oxygen as electron acceptor under microoxic conditions, indicates that MBH gene transcription is not regulated in contrast to other facultative hydrogen-oxidizing bacteria. The MBH showed quinone-reactivity and a characteristic UV/VIS spectrum implying a cytochrome b as membrane-integral subunit. Cell extracts of S. multivorans were subjected to native polyacrylamide gel electrophoresis (PAGE) and hydrogen oxidizing activity was tested by native staining. Only one band was detected at about 270 kDa in the particulate fraction of the extracts, indicating that there is only one hydrogen-oxidizing enzyme present in S. multivorans. An enrichment of this enzyme and SDS PAGE revealed a subunit composition corresponding to that of the MBH. From these findings we conclude that the MBH is the electron-donating enzyme system in the PCE respiratory chain. The roles for the other three hydrogenases remain unproven. The group 4 hydrogenase might be involved in hydrogen production upon fermentative growth.

A high-resolution anatomical atlas of the transcriptome in the mouse embryo.

Ascertaining when and where genes are expressed is of crucial importance to understanding or predicting the physiological role of genes and proteins and how they interact to form the complex networks that underlie organ development and function. It is, therefore, crucial to determine on a genome-wide level, the spatio-temporal gene expression profiles at cellular resolution. This information is provided by colorimetric RNA in situ hybridization that can elucidate expression of genes in their native context and does so at cellular resolution. We generated what is to our knowledge the first genome-wide transcriptome atlas by RNA in situ hybridization of an entire mammalian organism, the developing mouse at embryonic day 14.5. This digital transcriptome atlas, the Eurexpress atlas (http://www.eurexpress.org), consists of a searchable database of annotated images that can be interactively viewed. We generated anatomy-based expression profiles for over 18,000 coding genes and over 400 microRNAs. We identified 1,002 tissue-specific genes that are a source of novel tissue-specific markers for 37 different anatomical structures. The quality and the resolution of the data revealed novel molecular domains for several developing structures, such as the telencephalon, a novel organization for the hypothalamus, and insight on the Wnt network involved in renal epithelial differentiation during kidney development. The digital transcriptome atlas is a powerful resource to determine co-expression of genes, to identify cell populations and lineages, and to identify functional associations between genes relevant to development and disease.