Foraging preference of barnacle geese on endophytic tall and red fescues

Many grasses (Poaceae) have symbiotic fungal endophytes, which affect livestock by producing unpalatable or harmful secondary compounds. Less is known about the repelling effects of fungal endophytes on avian grazers despite potential wildlife management implications. Herbivorous goose (Branta spp.) species may become a nuisance in recreational use areas via fecal littering. Planting these areas with grasses that avian grazers avoid may help mitigate this damage. In 2016, we studied the foraging preference of the barnacle geese (B. leucopsis) with endophytic (E+) or endophyte-free (E-) red fescue (Festuca rubra) and/or tall fescue (Schedonorus phoenix) in 2 sites in Finland that had a history of nuisance geese damage. In the high grazing pressure site, we planted both grass species, while in the low grazing pressure site only tall fescue was used. Geese preference was measured as the percentage of the area grazed, the height of the residual grass grazed, and the number of fecal droppings in the grass plots. Geese foraging did not differ between E- and E+ grasses, but red fescues were preferred over tall fescues. This supports previous findings that tall fescues or other coarse species could reduce the attractiveness of recreational areas to geese

Differences in incubation behaviour and niche separation of two competing flycatcher species

Food availability sets the stage for incubation behaviour of a female bird and thereby indirectly determines the nest temperature, which in turn affects development and metabolism of avian embryos. Changes in development and metabolism in turn are known to influence offspring's ability to adjust to environmental changes later in life. However, few studies have investigated the role of interspecific differences in incubation behaviour in relation to niche separation between competing sibling species. We studied the effects of habitat quality (in terms of caterpillar availability) on incubation behaviour of two ecologically similar and closely related species, collared and pied flycatchers (Ficedula albicollisandF. hypoleuca), in their hybrid zone on the island of oland, Sweden. Even though both species prefer caterpillar-rich deciduous forests as nesting sites, collared flycatchers, whose nestlings have higher energetic demands, are able to nest only in deciduous forests, whereas pied flycatchers have more flexible habitat requirements. Overall, higher food availability was associated with increased nest attendance, higher incubation temperature and a lower number of foraging trips across species. In addition, collared flycatchers had more frequent and shorter foraging trips across habitat types, allocated more heat to eggs and therefore maintained higher nest temperatures compared to pied flycatchers. We argue that the higher heat allocation or the need to maintain a higher nest temperature for embryo development may constrain collared flycatchers to focus on relatively more profitable prey. Our results highlight the importance of considering incubation behaviour in the context of understanding species differences in niche use. Significance statement Niche separation plays an important role in mitigating effects of competition between closely related species. Whether species differences in incubation behaviour relate to differences in niche use remains unknown. We compared incubation behaviour of two sympatric flycatcher species that differ in sensitivity to food availability. The competitively more dominant and larger species, the collared flycatcher, whose nestlings are more sensitive to food shortages, made more frequent foraging trips but allocated more heat to eggs, leading to higher nest temperature despite lower nest attendance, compared to pied flycatchers. These interspecific differences may be a result of differences in embryo sensitivity or female physiology and contribute to the niche separation between the species, which in turn can facilitate coexistence

Flexor Hallucis Longus tendon rupture in RA-patients is associated with MTP 1 damage and pes planus

<p>Abstract</p> <p>Background</p> <p>To assess the prevalence of and relation between rupture or tenosynovitis of the Flexor Hallucis Longus (FHL) tendon and range of motion, deformities and joint damage of the forefoot in RA patients with foot complaints.</p> <p>Methods</p> <p>Thirty RA patients with painful feet were analysed, their feet were examined clinically for the presence of pes planus and range of motion (ROM), radiographs were scored looking for the presence of forefoot damage, and ultrasound examination was performed, examining the presence of tenosyovitis or rupture of the FHL at the level of the medial malleolus. The correlation between the presence or absence of the FHL and ROM, forefoot damage and pes planus was calculated.</p> <p>Results</p> <p>In 11/60(18%) of the feet, a rupture of the FHL was found. This was associated with a limited motion of the MTP1-joint, measured on the JAM (χ²= 10.4, p = 0.034), a higher prevalence of pes planus (χ²= 5.77, p = 0.016) and a higher prevalence of erosions proximal at the MTP-1 joint (χ²= 12.3, p = 0.016), and joint space narrowing of the MTP1 joint (χ²= 12.7, p = 0.013).</p> <p>Conclusion</p> <p>Rupture of the flexor hallucis longus tendon in RA-patients is associated with limited range of hallux motion, more erosions and joint space narrowing of the MTP-1-joint, as well as with pes planus.</p

Second law, entropy production, and reversibility in thermodynamics of information

We present a pedagogical review of the fundamental concepts in thermodynamics of information, by focusing on the second law of thermodynamics and the entropy production. Especially, we discuss the relationship among thermodynamic reversibility, logical reversibility, and heat emission in the context of the Landauer principle and clarify that these three concepts are fundamentally distinct to each other. We also discuss thermodynamics of measurement and feedback control by Maxwell's demon. We clarify that the demon and the second law are indeed consistent in the measurement and the feedback processes individually, by including the mutual information to the entropy production.Comment: 43 pages, 10 figures. As a chapter of: G. Snider et al. (eds.), "Energy Limits in Computation: A Review of Landauer's Principle, Theory and Experiments

Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error

Nuclear large subunit ribosomal DNA is widely used in fungal phylogenetics and to an increasing extent also amplicon-based environmental sequencing. The relatively short reads produced by next-generation sequencing, however, makes primer choice and sequence error important variables for obtaining accurate taxonomic classifications. In this simulation study we tested the performance of three classification methods: 1) a similarity-based method (BLAST + Metagenomic Analyzer, MEGAN); 2) a composition-based method (Ribosomal Database Project naïve Bayesian classifier, NBC); and, 3) a phylogeny-based method (Statistical Assignment Package, SAP). We also tested the effects of sequence length, primer choice, and sequence error on classification accuracy and perceived community composition. Using a leave-one-out cross validation approach, results for classifications to the genus rank were as follows: BLAST + MEGAN had the lowest error rate and was particularly robust to sequence error; SAP accuracy was highest when long LSU query sequences were classified; and, NBC runs significantly faster than the other tested methods. All methods performed poorly with the shortest 50–100 bp sequences. Increasing simulated sequence error reduced classification accuracy. Community shifts were detected due to sequence error and primer selection even though there was no change in the underlying community composition. Short read datasets from individual primers, as well as pooled datasets, appear to only approximate the true community composition. We hope this work informs investigators of some of the factors that affect the quality and interpretation of their environmental gene surveys

Species Used for Drug Testing Reveal Different Inhibition Susceptibility for 17beta-Hydroxysteroid Dehydrogenase Type 1

Steroid-related cancers can be treated by inhibitors of steroid metabolism. In searching for new inhibitors of human 17beta-hydroxysteroid dehydrogenase type 1 (17β-HSD 1) for the treatment of breast cancer or endometriosis, novel substances based on 15-substituted estrone were validated. We checked the specificity for different 17β-HSD types and species. Compounds were tested for specificity in vitro not only towards recombinant human 17β-HSD types 1, 2, 4, 5 and 7 but also against 17β-HSD 1 of several other species including marmoset, pig, mouse, and rat. The latter are used in the processes of pharmacophore screening. We present the quantification of inhibitor preferences between human and animal models. Profound differences in the susceptibility to inhibition of steroid conversion among all 17β-HSDs analyzed were observed. Especially, the rodent 17β-HSDs 1 were significantly less sensitive to inhibition compared to the human ortholog, while the most similar inhibition pattern to the human 17β-HSD 1 was obtained with the marmoset enzyme. Molecular docking experiments predicted estrone as the most potent inhibitor. The best performing compound in enzymatic assays was also highly ranked by docking scoring for the human enzyme. However, species-specific prediction of inhibitor performance by molecular docking was not possible. We show that experiments with good candidate compounds would out-select them in the rodent model during preclinical optimization steps. Potentially active human-relevant drugs, therefore, would no longer be further developed. Activity and efficacy screens in heterologous species systems must be evaluated with caution

TESTLoc: protein subcellular localization prediction from EST data

Abstract Background The eukaryotic cell has an intricate architecture with compartments and substructures dedicated to particular biological processes. Knowing the subcellular location of proteins not only indicates how bio-processes are organized in different cellular compartments, but also contributes to unravelling the function of individual proteins. Computational localization prediction is possible based on sequence information alone, and has been successfully applied to proteins from virtually all subcellular compartments and all domains of life. However, we realized that current prediction tools do not perform well on partial protein sequences such as those inferred from Expressed Sequence Tag (EST) data, limiting the exploitation of the large and taxonomically most comprehensive body of sequence information from eukaryotes. Results We developed a new predictor, TESTLoc, suited for subcellular localization prediction of proteins based on their partial sequence conceptually translated from ESTs (EST-peptides). Support Vector Machine (SVM) is used as computational method and EST-peptides are represented by different features such as amino acid composition and physicochemical properties. When TESTLoc was applied to the most challenging test case (plant data), it yielded high accuracy (~85%). Conclusions TESTLoc is a localization prediction tool tailored for EST data. It provides a variety of models for the users to choose from, and is available for download at http://megasun.bch.umontreal.ca/~shenyq/TESTLoc/TESTLoc.html</p

In Silico Insights into the Symbiotic Nitrogen Fixation in Sinorhizobium meliloti via Metabolic Reconstruction

BACKGROUND: Sinorhizobium meliloti is a soil bacterium, known for its capability to establish symbiotic nitrogen fixation (SNF) with leguminous plants such as alfalfa. S. meliloti 1021 is the most extensively studied strain to understand the mechanism of SNF and further to study the legume-microbe interaction. In order to provide insight into the metabolic characteristics underlying the SNF mechanism of S. meliloti 1021, there is an increasing demand to reconstruct a metabolic network for the stage of SNF in S. meliloti 1021. RESULTS: Through an iterative reconstruction process, a metabolic network during the stage of SNF in S. meliloti 1021 was presented, named as iHZ565, which accounts for 565 genes, 503 internal reactions, and 522 metabolites. Subjected to a novelly defined objective function, the in silico predicted flux distribution was highly consistent with the in vivo evidences reported previously, which proves the robustness of the model. Based on the model, refinement of genome annotation of S. meliloti 1021 was performed and 15 genes were re-annotated properly. There were 19.8% (112) of the 565 metabolic genes included in iHZ565 predicted to be essential for efficient SNF in bacteroids under the in silico microaerobic and nutrient sharing condition. CONCLUSIONS: As the first metabolic network during the stage of SNF in S. meliloti 1021, the manually curated model iHZ565 provides an overview of the major metabolic properties of the SNF bioprocess in S. meliloti 1021. The predicted SNF-required essential genes will facilitate understanding of the key functions in SNF and help identify key genes and design experiments for further validation. The model iHZ565 can be used as a knowledge-based framework for better understanding the symbiotic relationship between rhizobia and legumes, ultimately, uncovering the mechanism of nitrogen fixation in bacteroids and providing new strategies to efficiently improve biological nitrogen fixation