Magnitude and variability of process rates in fungal diversity-litter decomposition relationships

There is compelling evidence that losses in plant diversity can alter ecosystem functioning, particularly by reducing primary production. However, impacts of biodiversity loss on decomposition, the complementary process in the carbon cycle, are highly uncertain. By manipulating fungal decomposer diversity in stream microcosm experiments we found that rates of litter decomposition and associated fungal spore production are unaffected by changes in decomposer diversity under benign and harsher environmental conditions. This result calls for caution when generalizing outcomes of biodiversity experiments across systems. In contrast to their magnitude, the variability of process rates among communities increased when species numbers were reduced. This was most likely caused by a portfolio effect (i.e. statistical averaging), with the uneven species distribution typical of natural communities tending to weaken that effect. Curbing species extinctions to maintain ecosystem functioning thus can be important even in situations where process rates are unaffected

Riparian plant species loss alters trophic dynamics in detritus-based stream ecosystems

Riparian vegetation is closely connected to stream food webs through input of leaf detritus as a primary energy supply, and therefore, any alteration of plant diversity may influence aquatic ecosystem functioning. We measured leaf litter breakdown rate and associated biological parameters in mesh bags in eight headwater streams bordered either with mixed deciduous forest or with beech forest. The variety of leaf litter types in mixed forest results in higher food quality for large-particle invertebrate detritivores ('shredders') than in beech forest, which is dominated by a single leaf species of low quality. Breakdown rate of low quality (oak) leaf litter in coarse mesh bags was lower in beech forest streams than in mixed forest streams, a consequence of lower shredder biomass. In contrast, high quality (alder) leaf litter broke down at similar rates in both stream categories as a result of similar shredder biomass in coarse mesh bags. Microbial breakdown rate of oak and alder leaves, determined in fine mesh bags, did not differ between the stream categories. We found however aquatic hyphomycete species richness on leaf litter to positively co-vary with riparian plant species richness. Fungal species richness may enhance leaf litter breakdown rate through positive effects on resource quality for shredders. A feeding experiment established a positive relationship between fungal species richness per se and leaf litter consumption rate by an amphipod shredder (Gammarus fossarum). Our results show therefore that plant species richness may indirectly govern ecosystem functioning through complex trophic interactions. Integrating microbial diversity and trophic dynamics would considerably improve the prediction of the consequences of species loss

Temperature oscillation coupled with fungal community shifts can modulate warming effects on litter decomposition

Diel temperature oscillations are a nearly ubiquitous phenomenon, with amplitudes predicted to change along with mean temperatures under global-warming scenarios. Impact assessments of global warming have largely disregarded diel temperature oscillations, even though key processes in ecosystems, such as decomposition, may be affected. We tested the effect of a 5 degrees C temperature increase with and without diel oscillations on litter decomposition by fungal communities in stream microcosms. Five temperature regimes with identical thermal sums (degree days) were applied: constant 3 degrees and 8 degrees C; diel temperature oscillations of 5 degrees C around each mean; and oscillations of 9 degrees C around 8 degrees C. Temperature oscillations around 8 degrees C (warming scenario), but not 3 degrees C (ambient scenario), accelerated decomposition by 18% (5 degrees C oscillations) and 31% (9 degrees C oscillations), respectively, compared to the constant temperature regime at 8 degrees C. Community structure was not affected by oscillating temperatures, although the rise in mean temperature from 3 degrees to 8 degrees C consistently shifted the relative abundance of species. A simple model using temperature-growth responses of the dominant fungal decomposers accurately described the experimentally observed pattern, indicating that the effect of temperature oscillations on decomposition in our warming scenario was caused by strong curvilinear responses of species to warming at low temperature, particularly of the species becoming most abundant at 8 degrees C (Tetracladium marchalianum). These findings underscore the need to consider species-specific temperature characteristics in concert with changes in communities when assessing consequences of global warming on ecosystem processes

Metabolism of no-carrier-added 2-[18F]fluoro-L-tyrosine in rats

Background: Several fluorine-18 labelled fluoroamino acids have been evaluated as tracers for the quantitative assessment of cerebral protein synthesis in vivo by positron emission tomography (PET). Among these, 2-[18F]fluoro-L-tyrosine (2-[18F]Tyr) has been studied in mice at a low specific activity. Its incorporation into proteins is fast and metabolism via other pathways is limited. The present in vivo study was carried out in normal awake rats using no-carrier-added 2-[18F]Tyr. Under normal physiological conditions, we have studied the incorporation into proteins and the metabolism of the tracer in different brain areas. Methods: No-carrier-added 2-[18F]Tyr was administered to awake rats equipped with chronic arterial and venous catheters. The time course of the plasma activity was studied by arterial blood sampling. The biodistribution of the activity in the main organs was studied at the end of the experiment. The distribution of radioactive species in plasma and brain regions was studied by acidic precipitation of the proteins and HPLC analysis of the supernatant. Results: The absolute uptake of radioactivity in brain regions was homogenous. In awake rats, nocarrier-added 2-[18F]Tyr exhibits a fast and almost quantitative incorporation into the proteins fractions of cerebellum and cortex. In striatum, this incorporation into proteins and the unchanged fraction of the tracer detected by HPLC could be lower than in other brain regions. Conclusion: This study confirms the potential of 2-[18F]fluoro-L-tyrosine as a tracer for the assessment of the rate of protein synthesis by positron emission tomography. The observed metabolism suggests a need for a correction for the appearance of metabolites, at least in plasma

Properties of field functionals and characterization of local functionals

Functionals (i.e. functions of functions) are widely used in quantum field theory and solid-state physics. In this paper, functionals are given a rigorous mathematical framework and their main properties are described. The choice of the proper space of test functions (smooth functions) and of the relevant concept of differential (Bastiani differential) are discussed. The relation between the multiple derivatives of a functional and the corresponding distributions is described in detail. It is proved that, in a neighborhood of every test function, the support of a smooth functional is uniformly compactly supported and the order of the corresponding distribution is uniformly bounded. Relying on a recent work by Yoann Dabrowski, several spaces of functionals are furnished with a complete and nuclear topology. In view of physical applications, it is shown that most formal manipulations can be given a rigorous meaning. A new concept of local functionals is proposed and two characterizations of them are given: the first one uses the additivity (or Hammerstein) property, the second one is a variant of Peetre's theorem. Finally, the first step of a cohomological approach to quantum field theory is carried out by proving a global Poincar\'e lemma and defining multi-vector fields and graded functionals within our framework.Comment: 32 pages, no figur

Genome Evolution of a Tertiary Dinoflagellate Plastid

The dinoflagellates have repeatedly replaced their ancestral peridinin-plastid by plastids derived from a variety of algal lineages ranging from green algae to diatoms. Here, we have characterized the genome of a dinoflagellate plastid of tertiary origin in order to understand the evolutionary processes that have shaped the organelle since it was acquired as a symbiont cell. To address this, the genome of the haptophyte-derived plastid in Karlodinium veneficum was analyzed by Sanger sequencing of library clones and 454 pyrosequencing of plastid enriched DNA fractions. The sequences were assembled into a single contig of 143 kb, encoding 70 proteins, 3 rRNAs and a nearly full set of tRNAs. Comparative genomics revealed massive rearrangements and gene losses compared to the haptophyte plastid; only a small fraction of the gene clusters usually found in haptophytes as well as other types of plastids are present in K. veneficum. Despite the reduced number of genes, the K. veneficum plastid genome has retained a large size due to expanded intergenic regions. Some of the plastid genes are highly diverged and may be pseudogenes or subject to RNA editing. Gene losses and rearrangements are also features of the genomes of the peridinin-containing plastids, apicomplexa and Chromera, suggesting that the evolutionary processes that once shaped these plastids have occurred at multiple independent occasions over the history of the Alveolata

Circadian Preference Modulates the Neural Substrate of Conflict Processing across the Day

Human morning and evening chronotypes differ in their preferred timing for sleep and wakefulness, as well as in optimal daytime periods to cope with cognitive challenges. Recent evidence suggests that these preferences are not a simple by-product of socio-professional timing constraints, but can be driven by inter-individual differences in the expression of circadian and homeostatic sleep-wake promoting signals. Chronotypes thus constitute a unique tool to access the interplay between those processes under normally entrained day-night conditions, and to investigate how they impinge onto higher cognitive control processes. Using functional magnetic resonance imaging (fMRI), we assessed the influence of chronotype and time-of-day on conflict processing-related cerebral activity throughout a normal waking day. Sixteen morning and 15 evening types were recorded at two individually adapted time points (1.5 versus 10.5 hours spent awake) while performing the Stroop paradigm. Results show that interference-related hemodynamic responses are maintained or even increased in evening types from the subjective morning to the subjective evening in a set of brain areas playing a pivotal role in successful inhibitory functioning, whereas they decreased in morning types under the same conditions. Furthermore, during the evening hours, activity in a posterior hypothalamic region putatively involved in sleep-wake regulation correlated in a chronotype-specific manner with slow wave activity at the beginning of the night, an index of accumulated homeostatic sleep pressure. These results shed light into the cerebral mechanisms underlying inter-individual differences of higher-order cognitive state maintenance under normally entrained day-night conditions

Imprinted antibody responses against SARS-CoV-2 Omicron sublineages

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma-neutralizing antibodies against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5, and that breakthrough infections, but not vaccination alone, induce neutralizing antibodies in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains, whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months after infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant–neutralizing antibody that is a strong candidate for clinical development

Epstein-Barr Virus-Induced Gene 3 (EBI3): A Novel Diagnosis Marker in Burkitt Lymphoma and Diffuse Large B-Cell Lymphoma

The distinction between Burkitt lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL), two types of mature aggressive B-cell lymphomas that require distinct treatments, can be difficult because of forms showing features intermediate between DLBCL and BL (here called BL/DLBCL). They can be discriminated by the presence of c-myc translocations characteristic of BL. However, these are not exclusive of BL and when present in DLBCL are associated with lower survival. In this study, we show that Epstein-Barr virus-induced gene 3 (EBI3) is differentially expressed among BL and DLBCL. Analysis of gene expression data from 502 cases of aggressive mature B-cell lymphomas available on Gene Expression Omnibus and immunohistochemical analysis of 184 cases of BL, BL/DLBCL or DLBCL, showed that EBI3 was not expressed in EBV-positive or -negative BL cases, whereas it was expressed by over 30% of tumoral cells in nearly 80% of DLBCL cases, independently of their subtypes. In addition, we show that c-myc overexpression represses EBI3 expression, and that DLBCL or BL/DLBCL cases with c-myc translocations have lower expression of EBI3. Thus, EBI3 immunohistochemistry could be useful to discriminate BL from DLBCL, and to identify cases of BL/DLBCL or DLBCL with potential c-myc translocations

Deep Sequencing of MYC DNA-Binding Sites in Burkitt Lymphoma

BACKGROUND: MYC is a key transcription factor involved in central cellular processes such as regulation of the cell cycle, histone acetylation and ribosomal biogenesis. It is overexpressed in the majority of human tumors including aggressive B-cell lymphoma. Especially Burkitt lymphoma (BL) is a highlight example for MYC overexpression due to a chromosomal translocation involving the c-MYC gene. However, no genome-wide analysis of MYC-binding sites by chromatin immunoprecipitation (ChIP) followed by next generation sequencing (ChIP-Seq) has been conducted in BL so far. METHODOLOGY/PRINCIPAL FINDINGS: ChIP-Seq was performed on 5 BL cell lines with a MYC-specific antibody giving rise to 7,054 MYC-binding sites after bioinformatics analysis of a total of approx. 19 million sequence reads. In line with previous findings, binding sites accumulate in gene sets known to be involved in the cell cycle, ribosomal biogenesis, histone acetyltransferase and methyltransferase complexes demonstrating a regulatory role of MYC in these processes. Unexpectedly, MYC-binding sites also accumulate in many B-cell relevant genes. To assess the functional consequences of MYC binding, the ChIP-Seq data were supplemented with siRNA- mediated knock-downs of MYC in BL cell lines followed by gene expression profiling. Interestingly, amongst others, genes involved in the B-cell function were up-regulated in response to MYC silencing. CONCLUSION/SIGNIFICANCE: The 7,054 MYC-binding sites identified by our ChIP-Seq approach greatly extend the knowledge regarding MYC binding in BL and shed further light on the enormous complexity of the MYC regulatory network. Especially our observations that (i) many B-cell relevant genes are targeted by MYC and (ii) that MYC down-regulation leads to an up-regulation of B-cell genes highlight an interesting aspect of BL biology