The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Lying deadwood retention affects microhabitat use of martens (Martes spp.) in European mountain forests

<p><span>Biodiversity loss due to intensive timber production is a ubiquitous conservation issue across temperate and boreal forest ecosystems. Retention forestry, the retention of deadwood and old-growth features within production forest, is one management strategy that has been implemented in various countries around the world to conserve a wide range of taxa within managed forests. The success and ecological implications of retention forestry are currently subject to intensive investigation and while some taxa like birds and insects have already been studied frequently, larger mammals have obtained less attention. Pine martens are one of the few larger mammals in central Europe preferring older forest and potentially profiting directly from deadwood retention as a consequence of implemented retention forestry. The goal of our study was to assess the response of European marten species to deadwood retention in montane mixed forests. Using marten detection rates from camera traps on 135 research plots we assessed the response of martens to deadwood on three different spatial scales using generalized linear mixed models. We found no effect of lying deadwood on marten detections on the plot scale (one-hectare) or in a ten-meter radius around the camera traps. However, we found a significant increase in marten detections if logs (>10 cm) were directly in front and in view of the camera trap. Our results show that deadwood retention as a measure of retention forestry does affect microhabitat use of martens, but not stand selection during the growing season. Logs directly in view of the camera trap increase marten detection rates as martens choose to move and forage along fallen trees when they are available. When using camera trapping to collect data on martens, trap positioning in front of logs can heavily bias trapping results when unaccounted for.</span></p><p>Funding provided by: Deutsche Forschungsgemeinschaft<br>Crossref Funder Registry ID: https://ror.org/018mejw64<br>Award Number: GRK 2123</p><p><span>We set up camera traps on 135 predetermined 1-ha research plots. We used camera traps (<em>Bushnell Trophy Cam HD Aggressor Low Glow</em>) over five sampling rounds in spring (April-early July) and autumn (late August-November) from 2019 to 2021. The exact positions of the camera traps in the first sampling round were assigned randomly to one of three fixed points within the plot. Afterwards, cameras were shifted systematically among those positions. <span>We aggregated marten detections in events, which included a sequence of detection of the same species with less than five minutes between pictures. The sum of marten events is used as an index of relative abundance. Additionally, we assessed the presence/volume of deadwood at three different scales (view of the camera, 10 m radius of the camera, 1-ha plot). </span></span></p&gt

Effects of understory characteristics on browsing patterns of roe deer in central European mountain forests

Abstract Selective browsing by deer on young trees may impede the management goal of increasing forest resilience against climate change and other disturbances. Deer population density is often considered the main driver of browsing impacts on young trees, however, a range of other variables such as food availability also affect this relationship. In this study, we use browsing survey data from 135 research plots to explore patterns of roe deer (Capreolus capreolus) browsing pressure on woody plants in mountainous forests in central Europe. We fitted species‐specific generalised linear mixed models for eight woody taxa, assessing the potential effects of understory characteristics, roe deer abundance and lying deadwood on browsing intensity. Our study reveals conspecific and associational effects for woody taxa that are intermediately browsed by roe deer. Selective browsing pressure was mediated by preferences of plants, in that, browsing of strongly preferred woody taxa as for example mountain ash (Sorbus aucuparia) and of least preferred woody taxa, for example Norway spruce (Picea abies) was not affected by the surrounding understory vegetation, while browsing pressure on intermediately browsed species like for example silver fir (Abies alba) was affected by understory characteristics. Contrary to our expectations, roe deer abundance was only positively associated with browsing pressure on silver fir and bilberry (Vaccinium myrtillus), while all other plants were unaffected by deer abundance. Finally, we did not find an influence of lying deadwood volume on the browsing pressure on any woody‐plant species. Overall, our results indicate that patterns in browsing preference and intensity are species‐specific processes and are partly affected by the surrounding understory vegetation. Current management strategies that aim to reduce browsing pressure through culling may be inefficient as they do not address other drivers of browsing pressure. However, managers also need to consider the characteristics of the local understory vegetation in addition to deer abundance and design species‐specific plans to reduce browsing on woody plant taxa

Enabling Virtual Met Masts for wind energy applications through machine learning-methods

As wind is the basis of all wind energy projects, a precise knowledge about its availability is needed. For an analysis of the site-specific wind conditions, Virtual Meteorological Masts (VMMs) are frequently used. VMMs make use of site calibrated numerical data to provide precise wind estimates during all phases of a wind energy project. Typically, numerical data are used for the long-term correlation that is required for estimating the yield of new wind farm projects. However, VMMs can also be used to fill data gaps or during the operational phase as an additional reference data set to detect degrading sensors. The value of a VMM directly depends on its ability and precision to reproduce site-specific environmental conditions. Commonly, linear regression is used as state of the art to correct reference data to the site-specific conditions. In this study, a framework of 10 different machine-learning methods is tested to investigated the benefit of more advanced methods on two offshore and one onshore site. We find significantly improving correlations between the VMMs and the reference data when using more advanced methods and present the most promising ones. The K-Nearest Neighbors and AdaBoost regressors show the best results in our study, but Multi-Output Mixture of Gaussian Processes is also very promising. The use of more advanced regression models lead to decreased uncertainties; hence those methods should find its way into industrial applications. The recommended regression models can serve as a starting point for the development of end-user applications and services

IL-4Rα-Dependent Alternative Activation of Macrophages Is Not Decisive for <i>Mycobacterium tuberculosis</i> Pathology and Bacterial Burden in Mice

<div><p>Classical activation of macrophages (caMph or M1) is crucial for host protection against <i>Mycobacterium tuberculosis</i> (<i>Mtb</i>) infection. Evidence suggests that IL-4/IL-13 alternatively activated macrophages (aaMph or M2) are exploited by <i>Mtb</i> to divert microbicidal functions of caMph. To define the functions of M2 macrophages during tuberculosis (TB), we infected mice deficient for IL-4 receptor α on macrophages (LysM^creIL-4Rα^-/lox) with <i>Mtb</i>. We show that absence of IL-4Rα on macrophages does not play a major role during infection with <i>Mtb</i> H37Rv, or the clinical Beijing strain HN878. This was demonstrated by similar mortality, bacterial burden, histopathology and T cell proliferation between infected wild-type (WT) and LysM^creIL-4Rα^-/lox mice. Interestingly, we observed no differences in the lung expression of inducible nitric oxide synthase (iNOS) and Arginase 1 (Arg1), well-established markers for M1/M2 macrophages among the <i>Mtb</i>-infected groups. Kinetic expression studies of IL-4/IL-13 activated bone marrow-derived macrophages (BMDM) infected with HN878, followed by gene set enrichment analysis, revealed that the MyD88 and IL-6, IL-10, G-CSF pathways are significantly enriched, but not the IL-4Rα driven pathway. Together, these results suggest that IL-4Rα-macrophages do not play a central role in TB disease progression.</p></div

Increased acute bacterial burden and chronic pulmonary pathology in absence of IL-4Rα responsive macrophages following low-dose <i>Mtb</i> H37Rv infection

<p>. Wild-type (BALB/c), IL-4Rα^-/- and IL-4Rα macrophage cell-specific deficient mice (LysM^creIL-4Rα^-/lox) were infected with <i>Mtb</i> H37Rv (100 CFU/mouse) by aerosol (n = 12–13 mice/group). (A) Percentages in body weight change are shown. (B) Mice were sacrificed at 4 and 18 weeks PI to determine bacterial loads in the lungs and spleen. (C) Lung weight indexes are shown. (D) At 0, 4 and 18 weeks PI, formalin-fixed lung sections were stained with H&E. Original magnification: 40X. (E) Lung sections of 5 mice per group were evaluated for pulmonary histopathology scores and quantification of total lesion sizes. N.D. = not detectable. (F) IL-4Rα expression was measured by flow cytometry on alveolar macrophages (SiglecF⁺CD11c⁺) at 0 and 18 weeks PI (*<i>P</i> < 0.05, **<i>P</i> < 0.01). Data shown are representative (A, D, E and F) and pooled (B, C) from two independent experiments.</p

MyD88 and IL-6, IL-10, G-CSF-dependent pathway genes are significantly enriched in HN878 infected vs. non-infected macrophages

<p>. BMDM were stimulated with IL-4/IL-13 or left untreated. After 24 hours of stimulation, cells were infected with HN878. Total RNA was extracted at 4, 12 and 48 hours PI for microarray and GSEA analysis. Enrichment plots and heat maps for (A) MyD88, (B) IL-6, IL-10, G-CSF and (C) IL-4Rα pathway are shown. Enrichment analysis compared log2-fold changes in <i>Mtb</i>-infected samples vs. non-infected samples. The rows in heat maps are listed according to pre-ranking metric scores. Replicates shown are from two independent experiments.</p

No major differences in expression of iNOS, Arg1, lung immune cell populations and T cell proliferation between wild-type and macrophage cell-specific IL-4Rα deficient mice following low-dose <i>Mtb</i> H37Rv infection (100 CFU/mouse).

<p>(A) iNOS and Arg1 staining (brown colour) from lung sections collected at indicated times PI, original magnification: 40X. Lung sections from 5 mice/group were quantified. N.D. = not detectable. (B) iNOS and Arg1 expression on various immune cells were analysed by flow cytometry at 18 weeks PI (6–7 mice/group, *<i>P</i> < 0.05). (C) T cell proliferation with co-cultured CD11c-sorted macrophages from the lung tissue of naïve non-infected and mice infected with H37Rv (100 CFU/mouse) by aerosol at 4 and 18 weeks. Data shown in A is representative of two independent experiments and results obtained in B and C are from one experiment.</p

Similar mortality, inflammation, bacterial burden, Arg1/iNOS expression and T cell proliferation in wild-type and LysM^creIL-4Rα^-/lox mice following high dose infection with <i>Mtb</i> H37Rv

<p>. Wild-type (BALB/c) and IL-4Rα macrophage cell-specific deficient mice (LysM^creIL-4Rα^-/lox) were infected intranasally with high dose of 10⁴ CFU/mouse of <i>Mtb</i> H37Rv (n = 20/group). (A) Survival of infected mice was recorded weekly. (B) Individual bacterial titers (CFU/organ) with group medians are shown (*<i>P</i> < 0.05). (C) iNOS and Arg1 staining (brown colour) from lung sections collected at 3 and 10 weeks PI. Lung sections from 5 mice/group were quantified. Original magnification: 40X. N.D. = not detectable. (D) T cell proliferation with co-cultured CD11c-sorted macrophages from the lung tissue of naïve non-infected and 3 weeks infected mice. All data shown is representative of two independent experiments except for B which is representative of three independent experiments.</p