Enhancing structural complexity: An experiment conducted in the Black Forest National Park,Germany

We report on a structural complexity enhancement (SCE) experiment that was designed to test ecological restoration measures in the Black Forest National Park, Germany. The main goal was to understand as to whether the creation of standing and downed deadwood within previously managed, single-layered Norway spruce (Picea abies L.) forests accelerates the development of forest structure, richness, and diversity of a range of taxonomic groups. Here we introduce the experimental design and describe the development of stand structure including abundance and richness of tree-related microhabitats (TreMs) within 5 years after initiation of the experiment in October 2016. To enhance structural complexity in treatment plots, 10 trees per plot were toppled using a skidder winch, and another 10 trees were ring barked at a height of around 60 cm above ground level with a chainsaw. To monitor stand structure, we collected data on common forest attributes such as diameter at breast height (DBH), tree height, and TreMs of all trees in the six experimental and six control plots measuring 0.25 ha in size before the treatments were carried out in 2016 and again in 2020/21. We analyzed the abundance and richness of TreMs using generalized linear mixed models with DBH and treatment vs. control as predictors. The SCE treatment resulted in a significant increase in deadwood volumes (4.2 vs. 439.5 m³) as well as in TreM abundance and richness (increase of 0.74 TreMs per tree). This indicates that the SCE treatment was effective to increase biodiversity-relevant structures such as deadwood and TreMs, in previously managed Norway spruce-dominated stands. The ongoing monitoring of a range of taxonomic groups (birds, bats, small mammals, coleoptera, fungi, mosses, and vascular plants) in this experiment will demonstrate to what extent the enhancement in structural complexity will lead to an enrichment in species richness and diversity.     

Ultradian cycles in mice: definitions and links with REMS and NREMS

Sleep can be organized in two quite different ways across homeothermic species: either in one block (monophasic), or in several bouts across the 24 h (polyphasic). Yet, the main relationships between variables, as well as regulating mechanisms, are likely to be similar. Correlations and theories on sleep regulation should thus be examined on both types of sleepers. In previous studies on monophasic humans, we have shown preferential links between the number of ultradian cycles and the rapid eye movement sleep (REMS) time, rather than with its counterpart non-rapid eye movement sleep (NREMS). Here, the sleep of 26 polyphasic mice was examined, both to better describe the NREMS distribution, which is far more complex than in humans, and to replicate the analyses performed on humans. As in humans, the strongest links with the number of cycles were with REMS. Links were not significant with NREMS taken as a whole, although positive correlations were found with the NREMS immediately preceding REMS episodes and inversely significant with the residue. This convergence between monophasic and polyphasic patterns supports the central role played by REMS in sleep alternation.     

Early Prediction of Sepsis Incidence in Critically Ill Patients Using Specific Genetic Polymorphisms

Several diagnostic methods for the evaluation and monitoring were used to find out the pro-inflammatory status, as well as incidence of sepsis in critically ill patients. One such recent method is based on investigating the genetic polymorphisms and determining the molecular and genetic links between them, as well as other sepsis-associated pathophysiologies. Identification of genetic polymorphisms in critical patients with sepsis can become a revolutionary method for evaluating and monitoring these patients. Similarly, the complications, as well as the high costs associated with the management of patients with sepsis, can be significantly reduced by early initiation of intensive care.     

ZAP-70 Tyrosine Kinase Is Required for LFA-1–dependent T Cell Migration

The ZAP-70 tyrosine kinase is essential for T cell activation by the T cell receptor. We show that ZAP-70 is also required for migration of T cells that is dependent on the integrin LFA-1. Invasion of TAM2D2 T cell hybridoma cells into fibroblast monolayers, which is LFA-1–dependent, was blocked by overexpression of dominant-negative ZAP-70 and by piceatannol but not by herbimycin A. The Syk inhibitor piceatannol blocks the Syk homologue ZAP-70, which is expressed by TAM2D2 cells, with the same dose dependence as the inhibition of invasion. Dominant-negative ZAP-70 completely inhibited the extensive metastasis formation of TAM2D2 cells to multiple organs upon i.v. injection into mice. Migration of TAM2D2 cells through filters coated with the LFA-1 ligand ICAM-1, induced by 1 ng/ml of the chemokine SDF-1, was blocked by anti–LFA-1 mAb and also abrogated by dominant-negative ZAP-70 and piceatannol. In contrast, migration induced by 100 ng/ml SDF-1 was independent of both LFA-1 and ZAP-70. LFA-1 cross-linking induced tyrosine phosphorylation, which was blocked by dominant-negative ZAP-70 and piceatannol. We conclude that LFA-1 engagement triggers ZAP-70 activity that is essential for LFA-1–dependent migration.     

Using RAD seq for reconstructing phylogenies of highly diverged taxa: A test using the tribe Scandiceae (Apiaceae)

The angiosperm Apiaceae tribe Scandiceae includes four major clades—subtribes Daucinae, Ferulinae, Torilidinae, and Scandicinae—that originated ca. 20 Mya. Although all four subtribes are highly supported in molecular analyses, and morphological data indicate a sister relationship between Daucinae and Torilidinae, their branching order has not been resolved using standard Sanger multilocus data. Therefore, in this study, we test the utility of genomic RAD seq data in resolving deep phylogenetic relationships (up to 20 Mya) in Apiaceae subfamily Apioideae, with special emphasis on tribe Scandiceae using 12 representative species. We used two bioinformatic pipelines, pyRAD and RADIS (based on STACKS), to assemble RAD seq data and we tested the influence of various combinations of parameters on the robustness of the inferred tree topologies. Although different data processing approaches produced alignments with various amounts of missing data, they converged to two well‐supported topologies, irrespective of the phylogenetic method applied. Highly supported trees showed Scandicinae as sister to all other clades and indicated that Daucinae and Torilidinae are sister groups, thus confirming the relationship inferred from morphology. We conclude that the RAD seq method can be successfully used to resolve deep relationships formed 20 Mya within Apiaceae. We provide recommendations for parameter settings in RADIS and pyRAD for the analysis of taxa that have accumulated considerable genomic divergence.     

Distinct evolutionary trajectories of MHC class I and class II genes in Old World finches and buntings

Major histocompatibility complex (MHC) genes code for key proteins of the adaptive immune system, which present antigens from intra-cellular (MHC class I) and extra-cellular (MHC class II) pathogens. Because of their unprecedented diversity, MHC genes have long been an object of scientific interest, but due to methodological difficulties in genotyping of duplicated loci, our knowledge on the evolution of the MHC across different vertebrate lineages is still limited. Here, we compared the evolution of MHC class I and class II genes in three sister clades of common passerine birds, finches (Fringillinae and Carduelinae) and buntings (Emberizidae) using a uniform methodological (genotyping and data processing) approach and uniform sample sizes. Our analyses revealed contrasting evolutionary trajectories of the two MHC classes. We found a stronger signature of pervasive positive selection and higher allele diversity (allele numbers) at the MHC class I than class II. In contrast, MHC class II genes showed greater allele divergence (in terms of nucleotide diversity) and a much stronger recombination (gene conversion) signal. Gene copy numbers at both MHC class I and class II evolved via fluctuating selection and drift (Brownian Motion evolution), but the evolutionary rate was higher at class I. Our study constitutes one of few existing examples, where evolution of MHC class I and class II genes was directly compared using a multi-species approach. We recommend that re-focusing MHC research from single-species and single-class approaches towards multi-species analyses of both MHC classes can substantially increase our understanding MHC evolution in a broad phylogenetic context.Subject terms: Molecular evolution, Immunogenetics