Miracle-dz/UniFAR-FTUs huggingface dataset:
Predator effects on aquatic community assembly: disentangling the roles of habitat selection and post-colonization processes

Top predators are known to play an important role in the assembly of communities via two mechanisms: (1) by altering the colonization (or emigration) patterns of prey through behavioral habitat selection, and (2) by altering vital rates (e.g. mortality, birth) of prey after colonization. While both these mechanisms act to determine assembly, research has focused on either their combined overall effects (confounding them), or examined them singly. As a result, it remains unclear how these mechanisms act to sequentially shape community structure. In this study, we experimentally disentangle habitat selection and post-colonization effects of predaceous fish to test their independent and combined influence on the assembly of insect and larval amphibian communities in experimental freshwater habitats. Specifically, we ask, ‘do the behavioral choices of colonists continue to structure aquatic communities even after post-colonization processes have occurred? ’ Like previous studies, we found that colonization was strongly reduced by the presence of fish cues. More importantly, these effects of fish on prey colonization behavior combined independently with post-colonization processes to determine the overall effect of predators on community assembly. Although habitat selection and predation both reduced abundance and biomass of most taxa in the post-colonization communities, these factors had qualitatively different effects on aspects of trophic structure. Habitat selection altered the ratio of secondary to primary consumer abundance and biomass, while post-colonization predation drove strong trophic cascades not observed in response to habitat selection. Our results suggest that behavioral choices regarding habitat selection can have lasting and unique effects on the structure of aquatic communities.
Interaction between bioluminescence and denticles in sharks

Etmopterid and dalatiid sharks are among the most enigmatic bioluminescent organisms. They display thousands of epidermal light-producing organs (photophores) that form a diversity of patterns and are primarily controlled by hormones rather than by nerves, the condition in other animals. Various adaptive benefits have been proposed for the light produced by these epidermal organs including camouflage by counterillumination (ventral photophores), intraspecific communication (lateral photophores) and aposematism (dorsal spine-associated photophores). Like other shark species, etmopterids and dalatiids have their skin covered with placoid scales (denticles), which are known to be involved in various tasks including hydrodynamism, protection from predators and ectoparasites and reduction of substrate abrasion. In bioluminescent sharks these denticles have evolved peculiar squamation patterns that are thought to allow photophore accomodation. However, variations in the crown morphology of these structures lead to different degrees of interaction with the photophores and their light emission. Here, we investigated the link between four squamation patterns (internal scales, pavement-like, thorn-like and bristle-like) and several parameters across specimens from 37 shark species (≈75% of current bioluminescent shark diversity) in order to determine if denticle morphology influences photophore organisation and performances. Unexpectedly, pavement-like squamation is linked to higher photophore density and cover (but smaller photophore diameter), and overall photophore performance appears equivalent in external denticles. Future work including optical lithography and computational modelling, will attempt to understand how needle-like denticles, which form a dense external coverage, still allow the delivery of underlying photophore light.
Body size, biomic specialization and range size of African large mammals

Aim The goal of this paper is to examine the relationships between body size, biomic specialization and range size in the African large mammals, which are defined as all the African species corresponding to the orders Primates, Carnivora, Proboscidea, Perissodactyla, Hyracoidea, Tubulidentata, Artiodactyla and Pholidota.
Investigations into phosphodieterases as targets for antimalarial drug discovery

Phosphodiesterases are key enzymes in cyclic-nucleotide signalling pathways, regulating the levels of cAMP and cGMP in the cell. Cyclic nucleotides play an important role in regulating progression of the complex parasite life cycle. There are four Plasmodium PDEs, PDEα-δ. PDEβ has proved refractory to deletion and is predicted to be essential in asexual blood stages. PDEs α, γ and δ have been successfully disrupted in previous studies, which revealed stage-specific roles for PDEγ and PDEδ in the mosquito. PDEβ is a promising drug target due to the proven ability to create specific inhibitors for individual human PDEs (e.g. Viagra inhibits human PDE5), the established safety record of current inhibitors and the predicted essential nature of PDEβ in P. falciparum blood stages. The lack of useful reagents; knockout strains, tagged lines and recombinant proteins, has severely limited progress in this field. Conditional genetic disruption (required to study essential genes) is notoriously difficult in P. falciparum. This project has attempted to generate a conditional knock-out using the destabilisation domain system and the novel DiCre system, which involves recombinase-mediated genomic excision of the target DNA upon introduction of a drug. A PDEβ haemagglutanin (HA) tagged line has been successfully generated and used to investigate the cellular biology of PDEβ, including, the subcellular localisation and cyclic nucleotide specificity of PDEβ, which until now has remained speculative. A small library of PDE inhibitors generated by Pfizer has been evaluated using a parasite growth inhibition assay and a PDE assay, with compounds active at sub-micromolar concentrations against the parasite and the protein. These assays have used wild type parasites and also a PDEα KO line which has no obvious phenotype in blood stage parasites.
Efficacy of Beauveria bassiana (Bals.) Vuill. against the tarnished plant bug, Lygus lineolaris L., in strawberries

Beauveria bassiana has a high insecticidal potential to control the tarnished plant bug, Lygus lineolaris, a significant pest of strawberries. Screening experiments showed that L. lineolaris adults were susceptible to several B. bassiana isolates. Another screening test with Coleomegilla maculata, a natural enemy found in strawberries, was also performed in order to select the isolate having lower entomopathogenic impact on this insect. Based on data obtained from both insect species and on the ecozone origin of the B. bassiana isolates, INRS‐IP and INRS‐CFL isolates were selected for further experiments. The LC50 values of these two isolates against L. lineolaris adults were 7.8 × 105 and 5.3 × 105 conidia/ml, and average survival time (AST) values were 4.46 and 4.37 days at a concentration of 1 × 108 conidia/ml respectively. Results also indicated that L. lineolaris nymphs are susceptible to the selected isolates. During field experiments, using a randomized block design with four replicates, INRS‐IP and INRS‐CFL isolates were applied at two rates (1 × 1011 and 1 × 1013 conidia/ha) weekly during a period of 4 weeks. These multiple applications triggered a significant reduction of L. lineolaris nymphal populations in strawberries. Twenty‐four days after the first application, a significant difference was observed between the mean population densities of surviving nymphs in all B. bassiana‐treated plots (less than one insect per five plants) compared with those in control plots (four insects per five plants). During the field experiment, persistence of insecticidal activity and viability of B. bassiana conidia were also monitored. The results showed the presence of viable and infective conidia up to 6 days after each application on strawberry foliage. Moreover, the multiple applications of B. bassiana at the rate of 1 × 1013 conidia/ha triggered a significant reduction in strawberry fruit injuries induced by L. lineolaris feeding behaviour compared with the control plots.
Relationship between N2-fixation and heterocyst abundance and its relevance to the nitrogen budget of Lake 227

A significant relationship between seasonal N2-fixation rate and heterocyst abundance has been found in Lake 227 and can be modelled to estimate areal rates of N2-fixation based on the known historical phytoplankton records. Experimental imposition of low nitrogen (N): phosphorus (P) loading ratios stimulated N,-fixation. The N:P molar ratio of the internal pool of nutrients oscillates around a mean of 30:1, despite experimental loading ratios that vary from 13:1 to 0. Maintenance of this internal nutrient mass ratio requires preferential regeneration of N through time at all loading rates. Heterocystous, cyanobacteria blooms are most predictable during imposition of a very low external loading N:P ratio and high P loading relative to natural sources. Knowledge of the internal loading N:P ratio and relative contribution of internal and external loadings are required for predicting blooms at intermediate external N:P loading rates. The internal N:P ratio has fluctuated within narrow limits over 25 yr of ne.
Breeding value evaluation for milk production in Murrah buffaloes: Combined information on individual and its female relatives*

Information on 305-day (or less) milk yield records of 832 Murrah buffaloes spread over 26 years (1970-1995), maintained at the National Dairy Research Institute, Karnal, were analyzed to predict the breeding value of female based on its own information in combination with its other female relatives. The prediction of breeding value based only on individual's first lactation and average of first 2 lactations had the accuracy of 0.5991 and 0.7621 respectively. The accuracy of prediction increased as first lactation of dam and average of 2 paternal half-sisters' first lactation records were combined with individual's information. In that case, the accuracy of prediction of breeding value was 0.6340 and 0.7995 for combined relatives' information along with first lactation and average of first 2 lactation records of individual respectively. Considering the time, effort and resources spent and the accuracy obtained from the combined information, it was concluded that only individual's own information was ideal for evaluation of breeding value in Murrah females.
Plasma Levels of amyloid β proteins Aβ1–40 and Aβ1–42(43) are elevated in Down's syndrome

To investigate the effect of the overexpression of β‐amyloid precursor protein (APP) on the production of two major amyloid β protein (Aβ) species, Aβ40 and Aβ42(43), we measured amounts of Aβ1–40 and Aβ1–42(43) in the plasma from 44 patients with Down's syndrome (DS) (age, 19–61 years) and 66 age‐matched normal controls using enzyme‐linked immunosorbent assays. Plasma concentrations of both Aβ1–40 and Aβ1–42(43) were increased about 3‐fold and 2‐fold, respectively, in DS patients compared with normal controls. Especially, the increases in plasma Aβ1–40 in DS Patients were statistically higher than the 1.5‐fold increase one might predict based on the gene dose of APP in DS. These findings showed that both Aβ1–40 and Aβ1–42(43) are increased in plasma in DS patients, the former more than the latter, suggesting that overexpression of APP and/or other genes may have different effects on the production of these two Aβ species in DS.
Single large or several small marine reserves for the Caribbean spiny lobster

The ‘SLOSS’ debate—Single Large Or Several Small protected areas—remains unresolved. We used a heuristic model based on population dynamics of Caribbean spiny lobster in Exuma Sound, Bahamas, to compare impacts of regional reserve designs that configured 20% of available coastal habitat as either a randomly located single large reserve or a network of six small, randomly located reserves on three performance indicators (fishery yield, larval production, population growth rate) for a hypothetical overexploited lobster population. Two additional management strategies were considered: one reduced effort by 20% (without protected areas), and one did nothing. Effects were evaluated for two levels of hydrodynamic variability. In general, performance indicators ranked the management strategies, independent of hydrodynamic variability, from best to worst in the order (1) single large reserve (2) several small reserves (3) reduced effort (4) no management action, but differences were not always significant. Therefore, for the model regional system investigated here, a single large reserve is preferable to several small ones. We propose that this conservation strategy is most suitable at the regional scale (~100s of kilometres) and that such single, large regional reserves would function most effectively within a broadscale (~1000s of kilometres) reserve network, barring local catastrophes.
New interactions between RNA-binding proteins and non-coding stem-loop RNAs

s, Posters and Lectures FOX-2 binding to pre-miR-20b influences strand bias (May 2015). Zagalak JA, Dogar AM, Stoltz M, Towbin H, Imig J, Brunschweiger A,Erich M, Mohammadi Pejman, Allain F, Hall J. RNA Society Meeting 2015, Madison, WI, USA Interactions between RBFOX-2 and pre-microRNA-20b terminal loop (July 2013). Zagalak JA, Dogar AM, Stoltz M, Towbin H, Ghidossi S, Erich M, Allain F, Hall J. Swiss Pharma Science Day, Berne, Switzerland Investigation of loop-binding proteins that modulate microRNA maturation in human cells (February 2012). Zagalak JA, Towbin H, Stoltz M, Hall J. Doktorandentag IPW, ETH Zürich, Switzerland Antibiotic drug resistance lecture on beta-lactamases. (2013+2014). Zagalak JA. Introductory lecture and lab course in medicinal chemistry. BSc pharmaceutical sciences ETH study program. Extracurricular Publications Was is(s)t Religion? Hertig N, Bektas U, Bouhouch R, Hertig D, Khangsar T, Zagalak JA, Zahn S, Bokharouss I, Pettersson U, Stolwijk L, Goldberger M, Jehle V Premarupa K Terlemez C, Wenk M. (2012) Werd Verlag. ISBN 978-3-85932-690-3. Cookbook. Das Festmahl der Religionen. Zagalak JA. (2013) Der Sonntag. 1/2013. Newspaper article.
Managing crop margins for enhancing the presence of pollinators and natural enemies - the Spanish approach

Nowadays and in the last years, biodiversity matters have become relevant. Different approaches have been set up in agriculture for the benefit of wildlife, and especially for the pollinator conservation (Wratten et al, 2012). An way to introduce conservation measures for increasing biodiversity into agro-ecosystems is by managing the crop margins and introducing flowering plants (Kells et al, 2001; Rands et al 2011). These can offer food and shelter not only for pollinators but for natural enemies as well, helping to mitigate their decline and this has been widely documented (Biesmeijer et al., 2006; Potts et al, 2010). Five years ago the so called ‘Operation pollinator’ was launched, a European initiative sponsored by Syngenta, active in nine countries. In Spain, the Technical University of Madrid (UPM) and the National Research Council (CSIC) participated in Madrid aiming at identifying a suitable floral mixture and its impact on wild social and non-social pollinators. During a 3-year study in a rainfed barley crop we have initially identified an optimal floral mixture. The most suitable plant species concerning the blooming period and duration, the coverage and attraction of beneficial fauna were Borago officinalis L. , Calendula officinalis L. , Coriandrum sativus L. and Diplotaxis catholica L. Additionally we have revealed the influence of the floral plants on the number and diversity of pollinators visiting the crop margin. The diversity of visitor species was high and the most common insect orders were Hymenoptera and Diptera. Small solitary bees (< 1 cm long) outnumbered other hymenopteran groups such as honey bees, bumble bees and large solitary bees. And because Central Spain is very dry, we tested in a 2-year study the suitability of the floral mixture in an irrigated melon crop, as well as the influence on the production and quality of the crop. The role of artificial shelters placed near the crop were studied also. References
polymerization of actin: v.a new organelle, the actomere, that initiates the assembly of actin filaments in thyone sperm

Between the acrosomal vacuole and the nucleus is a cup of amorphous material (profilactin) which is transformed into filaments during the acrosomal reaction. In the center of this cup in untreated Thyone sperm is a dense material which I refer to as the actomere; it is composed of 20-25 filaments embedded in a dense matrix. To visualize the substructure of the actomere, the profilactin around it must be removed. This is achieved either by demembranating the sperm with Triton X-100 and then raising the pH to 8.0, or by adding ionophores to intact sperm at pH 8.0. Under these conditions, the actomere remains as a unit while the rest of the profilactin is solubilized or polymerized. When demembranated sperm are incubated under conditions in which the actin should polymerize, filaments grow from the end of the actomere: the actomere thus appears to behave as a nucleating body. This observation is strengthened by experiments in which untreated sperm are incubated in seawater or isotonic NaCl at pH 7.0 and the ionophore X537A is added; in this case, only a partial polymerization of the actin occurs and the acrosomal vacuole does not fuse with the cell surface. The actin filaments that do form, however, are attached to the apical end of the actomere. In fact, the elongating filaments push their way into and frequently through the acrosomal vacuole. Thus, it appears that the sperm organizes the actin filaments by controlling their nucleation. My model is that the cell controls the amount of unbound actin such that it is slightly above the critical concentration for polymerization. Then, spontaneous nucleation is unfavored and polymerization would proceed from existing nuclei such as the actomere.
Epigenetic PU.1 silencing in myeloid leukemia by mimicrying a T cell specific chromatin loop

zur Erlangung des akademischen Grades d o c t o r r e r u m n a t u r a l i u m 4.2 The +71 insulator function involves binding of chromatin organizers ____________ 92 4.2. 1 CTCF mediates the insulator function of the +71 element ______________________________ 92 4.2. 2 SatB1 binds the +71 element but is not necessary for insulation activity ___________________ 94 4.3 AML blasts adopt the T-cell specific insulating loop conformation ______________ 95 4.3. 1 The insulating loop is disrupted during differentiation of leukemic blasts __________________ 96 4.3. 2 PU.1 expression block is associated with the insulating loop in AML patients ______________ 97 I Abstract Alterations in the local chromatin structure orchestrate the dynamic regulation of differentiation promoting genes. PU.1 is a master transcription factor in hematopoiesis. PU.1 gene must be tightly regulated to achieve lineage specific expression pattern. High levels of PU.1 are required for myeloid commitment: it is expressed at intermediate level in B-cells and must be actively silenced to permit T cell development from early multipotent progenitors. However, little is known of how PU.1 is regulated in T-cells. Moreover, aberrant PU.1 expressions have been observed in multiple leukemias. Using a genome-wide chromatin interaction screen we identified a cis-repressor with insulating capacity that undergoes long-distant chromatin looping to block PU.1 promoter activity in T cells but not myeloid or B cells. Looping and repression requires binding of the chromatin regulator protein CTCF. In contrast to normal myeloid cells, we found that cancer cells from myeloid leukemia patients adopt the T cell specific repressive chromatin structure bringing the insulator into spatial contact with the PU.1 promoter. These results identify CTCF controlled long-distant insulator looping as a novel mechanism to silence lineage-opposing transcription factor expression, and reveal that cancer cells can mimic the chromatin confirmation of another lineage to block expression of differentiation driving genes. anderer Zelllinien imitieren können, um die Expression von Differenzierungsgenen zu blockieren. 1 Introduction 1.1 Gene regulation After the sequencing of the human genome had been essentially completed in 2001 (Lander et al., 2001; McPherson et al., 2001), the gene-centric paradigm shifted eventually to a genome-wide investigation, finally confirming the presence of gene networks, which define the effective transcriptome of specific cell populations (McPherson et al., 2001; Zhou et al., 2011). Moreover, comparative genome analysis revealed a surprisingly constancy in genetic content: vertebrate genomes contain only about twice the number of genes compared to …
Control de estabilidad basado en MPC para un vehículo eléctrico con motores en rueda

Hoy en día, el número de vehículos se está incrementando, lo que supone un problema dado que la gran mayoría de emisiones y de consumo de petróleo recae sobre ellos. Por esta razón la mayoría de fabricantes de coches investigan las posibilidades de la movilidad sostenible. Estas nuevas plataformas, tales como vehículos eléctricos e híbridos, cobran cada vez más importancia debido a su mayor eficiencia termodinámica.
Protein–protein interactions of the cytochrome c oxidase DNA barcoding region

Enzymatic amplification of homologous regions of DNA using ‘universal’ polymerase chain reaction primers has provided insight into insect systematics, phylogeography, molecular evolution and species identification. One of the more commonly amplified and sequenced regions is a short region of the cytochrome c oxidase subunit I gene (COI), commonly called the barcoding region. COI is one of three mitochondrial‐encoded subunits of complex IV (Cox) of the electron transport chain. In addition to the mitochondrial subunits there are nine nuclear‐encoded subunits of the complex in Drosophila. Whereas a number of phylogenetic biases associated with this region have been examined and the quaternary structure of Cox has been modelled, the influence of protein–protein interactions on the observed patterns of evolution in this barcoding region of insects has never been examined critically. Using a well‐resolved independently derived phylogeny of 38 Diptera species, we examined the homogeneity of the substitution processes within the barcoding region. We show that, within Diptera, amino acid residues interacting with nuclear‐encoded subunits of Cox are evolving at elevated rates across the phylogeny. Furthermore, we show that codon position two is biased by protein–protein interactions. In contrast, third codon positions provide a less biased estimate of genetic variation in the region. This study highlights the need to examine the potential for systematic bias in DNA barcoding regions as part of the critical assessment of evidence in systematics and in biodiversity assessments.