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opencc-by-4.0Mar 2024View details →

Genomics polymorphisms of Staphylococcus aureus strain NCTC 8325 in the lab stock maintained at TUM (WT), after 30 passes in BHI media (D) and after 30 passes detecting 4 -fold MIC increase to isocyanide -code I16- 3 biological replicates (A,B,C), and 3 independent colonies sequenced per replicate at the end of the experiment.

Genomics polymorphisms of Staphylococcus aureus strain NCTC 8325 in the lab stock maintained at TUM (WT), after 30 passes in BHI media (D) and after 30 passes detecting 4 -fold MIC increase to isocyanide -code I16-  3 biological replicates (A,B,C), and 3 independent colonies sequenced per replicate at the end of the experiment. Determined from Illumina shotgun genomic sequencing datasets, mapping and analyses vs the reference genome of the strain https://www.ncbi.nlm.nih.gov/nuccore/NC_007795.1/

opencc-zeroMar 2024View details →

Brain–muscle tissue communication prevents muscle aging by maintaining daily physiology

A network of molecular clocks is crucial for coordinating daily physiology and maintaining organismal health. However, the mechanisms underlying the interactions between these clocks and the significance of intra-tissue clock networks in muscle tissue maintenance have remained elusive. To uncover this network structure, we established a minimal clock module with the central clock (suprachiasmatic nucleus/brain) and/or a peripheral clock (muscle) in arrhythmic mice with premature aging. We find that reconstituting the brain-muscle clock network alone is sufficient to preserve fundamental daily homeostatic functions and prevent premature muscle aging. However, achieving whole muscle daily physiology requires the contribution of other peripheral clocks. Mechanistically, the muscle peripheral clock acts as a gatekeeper, selectively suppressing signals from the central clock that could be detrimental to muscle function if left uncontrolled while also integrating important muscle homeostatic functions. Our findings unveil the reciprocal interactions between central and peripheral clocks crucial for daily muscle function and highlight the significant influence of eating patterns on these interactions. These insights have implications for promoting healthier aging and reversing age-related muscle pathologies.

opencc-zeroJan 2022View details →

Post-association barrier to host switching maintained despite strong selection in a novel mutualism

Following a host shift, repeated co-passaging of a mutualistic pair is expected to increase fitness over time in one or both species. Without adaptation, a novel association may be evolutionarily short-lived as it is likely to be outcompeted by native pairings. Here we test whether experimental evolution can rescue a low-fitness novel pairing between two sympatric species of Steinernema nematodes and their symbiotic Xenorhabdus bacteria. Despite low mean fitness in the novel association, considerable variation in nematode reproduction was observed across replicate populations. We selected the most productive infections, co-passaging this novel mutualism nine times to determine whether selection could improve fitness of either or both partners. We found that neither partner showed increased fitness over time. Our results suggest that the variation in association success was not heritable and that mutational input was insufficient to allow evolution to facilitate this host shift. Thus, post-association costs of host switching may represent a formidable barrier to novel partnerships among sympatric mutualists.

opencc-zeroFeb 2022View details →

Wild legumes maintain beneficial soil rhizobia populations despite decades of nitrogen deposition

Natural landscapes are increasingly impacted by nitrogen enrichment from aquatic and airborne pollution sources. Nitrogen enrichment in the environment can eliminate the net benefits that plants gain from nitrogen-fixing microbes such as rhizobia, potentially altering host-mediated selection on nitrogen fixation. However, we know little about the long-term effects of nitrogen enrichment on this critical microbial service. Here, we sampled populations of the legume Acmispon strigosus and its associated soil microbial communities from sites spanning an anthropogenic nitrogen deposition gradient. We measured the net growth benefits plants obtained from their local soil microbial communities and quantified plant investment into nodules that house nitrogen-fixing rhizobia. We found that plant growth benefits from sympatric soil microbes did not vary in response to local soil nitrogen levels, and instead varied mainly among plant lines. Soil nitrogen levels positively predicted the number of nodules formed on sympatric plant hosts, although this was likely due to plant genotypic variation in nodule formation, rather than variation among soil microbial communities. The capacity of all the tested soil microbial communities to improve plant growth is consistent with plant populations imposing strong selection on rhizobial nitrogen fixation despite elevated soil nitrogen levels, suggesting that host control traits in A. strigosus are stable under long-term nutrient enrichment.

Figure 9 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)

Figure 9. Five sequential matings (1-2, 3, 4, 5-6, 7) of the two male forms with the same female Maevia inclemens over the course of five days. 1-2, This mating was interrupted as the male switched from one side to the other, but after an atypical low crawl display with legs I extended, the tufted male quickly recaptured the female and continued to mate on the other side. 5-6, mating on the right and then left sides. Note the many erect spines on the legs of the mating male in each instance.

Figure 8 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)

Figure 8. Sequential positions (1-4) of the tufted male Maevia inclemens as he advanced toward the female in a still later mating attempt (after Figure 7). Here the view of the female is shown. 1-2, Waving legs I. 3, Fully extended for maximum height. 4, Display from a lower position with raised legs I.

Figure 3 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)

Figure 3. Adult male Maevia inclemens, tufted (black) form. The tufts of the dorsal carapace may not be present in all males of this form. Note the lack of stripes on the uniformly-colored legs. 2, Feeding on mosquito (Diptera: Culicidae).

Figure 4 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)

Figure 4. Four sequential positions of a male (1-4) during the successful courtship of a female Paraphidippus aurantius (Lucas 1833) on a plant in the laboratory. Males were placed on plants with three recently molted females, all from Greenville County, South Carolina. In each case the female stopped moving soon after she sighted the male, and the male advanced to mate successfully when she did not turn to face him as he stepped from side to side. In this example the female stopped moving at a distance of about 10 cm from the approaching male. The subsequent mating included insertion of each pedipalp on the respective side of the epigynum, and occupied more than 20 minutes. P. aurantius males will cohabit with and defend penultimate females (Thurlow 2016), and their large chelicerae are associated with the ritual male-male combat (agonistic behavior) that may ensue. This represents a pattern seen in many other salticids (e.g., Lyssomanes viridis, Tedore & Johnsen 2012, 2013, 2015), in which male-male contests account for most sexual selection. At the other end of the spectrum of sexual selection lie the highly ornamented salticids of the genus Maratus, for which male-male contests are virtually unknown (save one species), and a female may examine the details of male ornamentation up-close before acceptance (Otto & Hill 2021). Most salticids appear to fall somewhere between these two extremes, relying to some extent on both male-male combat and active selection by females.

Figure 1. Adult female Maevia inclemens. 1-2, 6 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)

Figure 1. Adult female Maevia inclemens. 1-2, 6, Feeding on a small fly (Diptera: Brachycera). 3-4, Feeding on a small robber fly (Diptera: Ascilidae). With the exception of Figure 5:8, only three M. inclemens individuals, two males and one female, all photographed on plants in the laboratory, are shown in this paper. All were collected in Massachusetts, June 2020.

Figure 7 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)

Figure 7. Sequential positions (1-10) of the tufted male Maevia inclemens as he advanced toward the female in a later mating attempt (after Figure 6).

Figure 10 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)

Figure 10. Attempted mating by the grey male Maevia inclemens. This sequence shows how the male jumped the female while she was suspended from her dragline, just after capturing a fly (1), and attempted to mate with her (2). The female promptly released her prey, and the male then fed on it for many minutes (3-4), still in a suspended position [23 JUNE 2020 14:09- 14:13]. Three days later this male approached and mated successfully with the female for a second time (Figures 5:1-7, 9:7).

Figure 5 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)

Figure 5. Display by grey males, Maevia inclemens. 1-7, Successive (low crawl) positions of the grey male male from Massachusetts, advancing to successfully mate with the female. When close, this male jumped and captured the female (Figure 9:7). 8, Display by a grey male from Sherburne County, Minnesota, recorded in 1982.

Figure 2 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)

Figure 2. Adult male Maevia inclemens, grey (striped) form. Note the stripes on the prolateral surface of each femur.

Figure 11 in Stabilizing selection to maintain the two male forms of the jumping spider Maevia inclemens (Araneae: Salticidae: Marpissina)

Figure 11. Sequential (1-2) views of encounter between the two male forms of Maevia inclemens. Apart from a brief defensive reaction by the grey male (2), no ritual combat ensued and the males did not appear to recognize that they were conspecific.

opencc-zeroMar 2022View details →

Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection

Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, MATA and MATB. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus Trichaptum (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three Trichaptum species. We characterized the chromosomal location of MATA and MATB, the molecular structure of MAT regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple MAT alleles segregating before the speciation event of Trichaptum species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. In vitro crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in Trichaptum is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.

opencc-zeroApr 2022View details →

Proteomic analysis of serum markers in patients maintained on Antipsychotics

Background: Schizophrenia (SZ) and bipolar disorder (BD) share many features: overlap in mood and psychotic symptoms, common genetic predisposition, treatment with antipsychotics (APs), and similar metabolic comorbidities. The pathophysiology of both is still not well defined, and no biomarkers can be used clinically for diagnosis and management. This study aimed to assess the plasma proteomics profile of patients with SZ and BD maintained on APs compared to those who had been off APs for six months and to healthy controls (HCs). Methods: We analyzed the data using functional enrichment, random forest modeling to identify potential biomarkers, and multivariate regression for the associations with metabolic abnormalities. Results: We identified several proteins known to play roles in the differentiation of the nervous system like NTRK2, CNTN1, ROBO2, and PLXNC1, which were downregulated in AP-free SZ and BD patients but were "normalized" in those on APs. Other proteins (like NCAM1 and TNFRSF17) were "normal" in AP-free patients but downregulated in patients on APs, suggesting that these changes are related to medications' effects. We found significant enrichment of proteins involved in neuronal plasticity, mainly in SZ patients on APs. Most of the proteins associated with metabolic abnormalities were more related to APs use than having SZ or BD. The biomarkers identification showed specific and sensitive results for schizophrenia, where two proteins (PRL and MRC2) produced adequate results. Conclusions: Our results confirmed the utility of blood samples to identify protein signatures and mechanisms involved in the pathophysiology and treatment of SZ and BD.

opencc-zeroMay 2022View details →

Song complexity is maintained during inter-population cultural transmission of humpback whale songs

Among animal species, the songs of male humpback whales (Megaptera novaeangliae) are a rare example of social learning between entire populations. Understanding fine-scale similarity in song patterns and structural features will better clarify how accurately songs are learned during inter-population transmission. Here, six distinct song types (2009–2015) transmitted from the east Australian to New Caledonian populations were quantitatively analysed using fine-scale song features. Results found that New Caledonian whales learned each song type with high accuracy regardless of the pattern's complexity. However, there were rare instances of themes (stereotyped patterns of sound units) only sung by a single population. These occurred more often in progressively changing 'evolutionary' songs compared to rapidly changing 'revolutionary' songs. Our results suggest that populations do not need to reduce complexity to accurately learn song patterns. Populations may also incorporate changes and embellishments into songs in the form of themes which are suggested to be learnt as distinct segments. Maintaining complex song patterns with such accuracy suggests significant acoustic contact, supporting the hypothesis that song learning may occur on shared feeding grounds or migration routes. This study improves the understanding of inter-population mechanisms for large-scale cultural transmission in animals.

opencc-zeroMay 2022View details →

A gas-only bioreactor system maintains stable culture environments and reveals that moderate pH deviations trigger transcriptome-wide responses in human cells cultured in physioxia and physiological buffers

Although pH instability is emerging as a potential driver of changes in cell physiology, pH is still poorly controlled during cell culture and in vitro experiments. Standard procedures include the use of chemicals usually not present in the primary physiological buffering system (CO2/HCO3-), such as acids and bases, to manipulate pH levels. This, however, leads to artifacts that potentially affect scientists' findings. Here, we propose a novel method for controlling pH levels by relying only on the physiological buffering system. pH was manipulated in a repurposed commercial bioreactor set-up, using a two-sided control loop of CO2 and N2 gas in NaHCO3--buffered medium. This method produces optimal and stable dO2 profiles and tightly maintains pH levels. With this procedure, we analyzed the effects of different pH levels (6.8, 7.0, 7.2, and 7.4) on the performance and transcriptome of the human GM12878 cell line over a 72-hours experiment. Our results showed that inflammation and negative cellular proliferation are among the signatures activated at low pH. This further highlights the importance of a thorough pH control during cell culture.

opencc-zeroJun 2022View details →

Data from: Small but mighty: how overlooked small species maintain community structure through middle Eocene climate change

Understanding current and future biodiversity responses to changing climate is pivotal as anthropogenic climate change continues. This understanding is complicated though by the multitude of available metrics to quantify dynamics, and by biased sampling protocols. Here, we investigate the impact of sampling protocol strategies using a data-rich fossil record to calculate effective diversity using Hill numbers for the first time on Paleogene planktonic foraminifera. We sample 22,830 individual tests, in two different size classes, across a seven-million-year time slice of the Middle Eocene featuring a major transient warming event, the Middle Eocene Climatic Optimum (MECO; ~40 million years ago (Ma)), at study sites in the mid-latitude North Atlantic. Using Generalized Additive Models (GAMs), we investigate community responses to climatic fluctuations. After correcting for any effects of fossil fragmentation, we show a peak in generic diversity in the early and mid-stages of the MECO as well as divergent trajectories between the typical size-selected community (> 180 µm) and a broader selection including smaller genera (> 63 µm). Assemblages featuring smaller genera are more resilient to the climatic fluctuations of the MECO than those assemblages that feature only larger genera, maintaining their community structure at the reference Hill numbers for Shannon's and Simpson's Index. These results raise fundamental questions about how communities respond to climate excursions. In addition, our results emphasise the need to design studies with the aim of collecting the most inclusive data possible, to allow detection of community changes and determine which species are likely to dominate future environments.