Miracle-dz/UniFAR-FTUs huggingface dataset:
Length and time scales of cell-cell signaling circuits in agar

A community of genetically heterogeneous cells embedded in an unmixed medium allows for sophisticated operations by retaining spatial differentiation and coordinating division-of-labor. To establish the principles of engineering reliable cell-cell communication in a heterogeneous environment, we examined how circuit parameters and spatial placement affect the range of length and time scales over which simple communication circuits interact. We constructed several “sender” and “receiver” strains with quorum-sensing signaling circuits. The sender cell colony produces acyl homoserine lactones (AHL), which diffuse across the semisolid medium. The receiver cell colony detects these signal molecules and reports by fluorescence. We have found that a single colony of one sender variant is sufficient to induce receiver response at more than 1.5cm separation. Furthermore, AHL degradase expression in receiver colonies produces a signal threshold effect and reduces the response level in subsequent receiver colonies. Finally, our investigation on the spatial placement of colonies gave rise to the design of a multicellular long-range communication array consisting of two alternating colony types. Its signal response successfully propagated colony-by-colony along a six-colony array spanning 4.8cm at a transmission velocity of 12.8 hours per colony or 0.075cm per hour. In addition, we have developed a reaction-diffusion model that recreates the observed behaviors of the many performed experiments using data-informed parameter estimates of signal diffusion, gene expression, and nutrient consumption. These results demonstrate that a mixed community of colonies can enable new patterning programs, and the corresponding model will facilitate the rational design of complex communication networks.
Estimation of vitamin C human protective dose for acetaminophen toxicity, using acute animal toxicity study

Acetaminophen (APAP) is the main cause of fulminant hepatic failure. Vitamin C is a natural antioxidant with protective potentials against APAP toxic damage. In this animal study, and after an LD50 determination and selection of suitable lethal dose, the investigation was done to select a proper protective dose of vitamin C against lethal APAP dose. All 6 animal groups received a lethal dose of APAP (3250 mg/kg), group II, III and IV received 500, 1000 and 1500 mg/kg vitamin C respectively, group V received 1200 mg/kg N-Acetylcysteine (NAC), and group VI receive 1000 mg/kg vitamin C and 1200 mg/kg NAC. Mortality was recorded and liver histopathology was carried out. The results showed, the mortality rate in the group I was 68.75% and 37.5%, 31.25% in group II and III respectively, while group IV Showed a higher mortality rate and in group V and VI it was 25%. There was also a gradual reduction in the grade of histopathological damage in all groups, ranging from 2.4 ± 0.55 in group I to 0.4 ± 0.55 in group V and VI. In conclusion, vitamin C showed an increasing reduction in mortality and more histopathological protection, and it was more significant at 1000 mg/kg. NAC adds no more protection or reduction in mortality. The estimated protective dose of vitamin C was 700 to1127 mg for each gram of APAP. Incorporation of this dose of vitamin C with APAP preparations may be considered as a promising method for reducing mortality or severity of APAP intoxication.
Genetic diversity of Gossypium barbadense from the central Brazilian Amazon

The Amazon Basin is a center of diversity of Gossypium barbadense and the strategy for conservation of this genetic resource depends on the knowledge of the diversity maintained in Amazonas State. During two expeditions, in 2012 and 2014, plants were collected in ten municipalities in the state of Amazonas, in the central Brazilian Amazon region. The molecular diversity was estimated by SSR markers for 50 samples collected in 2012. The morphological diversity of 24 plants collected in 2014 was assessed ex situ and compared to that of 50 plants of the same and other cotton varieties from other Brazilian states. Most of plants evaluated in situ in Amazonas had purple petioles and veins (82%), associated to medicinal use, and kidney seeds (78%). The ex situ morphological analysies showed that G. barbadense plants from the Amazonas state: i) presented higher similarity to cotton plants from other northern Brazilian states, and ii) were grouped separately from those of other northern Brazilian states by descriptor analysis. Both the molecular (H=0.41) and morphological (H=0.38±0.02) diversity among the collected plants was considered intermediary. Our study indicates the distinctiveness of Amazon cottons, and contributes to demonstrate the discrimination power of multicategorical traits.
Differential Gene expression Study of Heat Shock Factors (Hsfs) in Heat Resistant Rice (Oryza sativa (L.)) Genotype IR 64

Rice (Oryza sativa (L.)) is the one of the most important cereal crops, providing staple food for nearly one-half of the global population. Global warming has great effects on plants and agriculture. The optimum temperature for the normal development of rice ranges from 27 to 32oC (Yin et al., 1996). By the end of the 21 Century, the earth’s climate is predicted to be warmer by an average of 2-4oC (Pachauri et al., 2007), due to both anthropogenic and natural factors (Eitzinger et al., 2010). As plants cannot move, the only option they have to defend themselves from various stresses is to make metabolic and structural adjustments (Yamanouchi et al., 2002). The environmental fluctuations greatly influence the phenotypic expression of the traits in varying degrees and thus exhibit variability in adoption across locations (Reddy et al., 2015). Yield losses can be overcome by integrated use of conventional and biotechnological approaches (Pawar et al., 2015). At the molecular level the heat-shock response is a transient reprogramming of cellular activities featured by the synthesis of Heat shock protein (Schoffl et al., 1998). Heat stress transcription factors (Hsfs) are the central regulators of defense response. They control the expression of heat shock proteins (HSPs) in plants by specific binding to the highly conserved heat shock element (HSE) characterized by palindromic motifs of nGAAn (Miller and Mittler, 2006). The basic structure and promoter recognition of Hsfs are highly conserved throughout the eukaryotic kingdom (Von Koskull-Doring et al., 2007). A typical Hsf protein contains a modular structure with an N-terminal DNA-binding domain (DBD), an adjacent bipartite oligomerization domain composed of Heptads repeat of hydrophobic amino acid residues (HR-A/B), a nuclear localization signal (NLS) essential for nuclear uptake of the protein, a nuclear export signal (NES), and in many cases a less conserved C-terminal activation domain (CTAD) rich in aromatic, hydrophobic and acidic amino acids (AHA) that have been reported to be crucial for activation function (Nover et al., 2001). Plant Hsf gene family is divided into three classes, HsfA, HsfB, and HsfC, according to their protein structures (Nover et al., 2001). HsfA and HsfC have insertions of 21 and 7 amino acids, between the hydrophobic regions HR-A and HR-B, respectively. HsfB and HsfC are also characterized by lack of AHA motifs in their C-terminal regions (CTRs). HsfA members are capable of transcriptional activation, while HsfB members act as repressors or as co-activators (e.g., HsfB1) of HsfA members (Bharti et al., 2004; Czarnecka-Verner et al., 2004).
Quantitative variation in female sensory structures supports species recognition and intraspecific mate choice functions in damselflies

Males and females exchange signals prior to mating that convey information such as sex, species identity, or individual condition. Tactile signals relayed during physical contact between males and females before and during mating appear to be important for mate choice and reproductive isolation in some animals. However, compared to our understanding of visual, auditory, and chemical signals, we know little about the importance of tactile signals in mating decisions. Among North American damselflies in the genus Enallagma (Odonata: Coenagrionidae) species-specific tactile stimulation contributes to reproductive isolation between species and may also be important for intraspecific mate choice. We quantified several mechanosensory sensilla phenotypes on the female thorax among multiple sympatric and allopatric populations of two Enallagma species that occasionally interbreed in nature. Although each species differed in features of sensilla distribution within the thoracic plates, we found no strong evidence of reproductive character displacement among the sensilla traits we measured in regions of sympatry. However, substantial variation of sensilla traits was observed within populations of both species. Our results suggest that species-specific placement of female mechanoreceptors appears sufficient for species recognition, but mechanosensor variation among females within species may be important for mate choice.
Cryoprotective Effect of Glycerol Concentrations on Indian Red Jungle Fowl (Gallus Gallus Murghi) Spermatozoa

Semen cryopreservation protocols for wild avian species need to be optimised in order to achieve optimum post-thaw sperm quality and fertility. The present study was designed to evaluate the cryoprotective effect of different glycerol concentrations (11%, 15% and 20%) on post-thaw quality, recovery rates, absolute livability index and fertility of Indian Red Jungle Fowl (Gallus gallus murghi) semen. Semen was collected from eight mature cocks and cryopreserved for storage at −196 °C. Frozen semen was thawed at 37 °C for 30 s and assessed for motility, plasma membrane integrity, viability and acrosome integrity at 0, 2 and 4 h incubation at 37 °C. Percentages of motility, plasma membrane integrity, viability and acrosome integrity were recorded higher (P<0.05) post-thaw at 0, 2 and 4 h at 37 °C with 20% glycerol compared to 15% and 11% glycerol. Likewise, recovery rates (%) of aforementioned parameters after cryopreservation and absolute livability index were observed highest (P<0.05) with 20% glycerol. By comparing values of R2 after multivariate regression analysis, least negative effects of hours of incubation were observed on semen quality in extenders with 20% glycerol followed by 15% and 11% glycerol. The fertility outcomes (number of fertile eggs, fertility [%], number of hatched chicks, percent hatch and hatchability of fertilised eggs) were recorded higher (P<0.05) with 20% glycerol followed by 15% and 11% glycerol. It is concluded that the concentration of 20% glycerol gives the best cryoprotection for quality and fertility of Indian Red Jungle Fowl semen.
Mammalia, Chiroptera, Phyllostomidae, Vampyrum spectrum (Linnaeus, 1758): first record for the Cerrado biome in the state of Mato Grosso, west central Brazil

In Brazil, Vampyrum spectrum has been recorded in the Amazon forest, Caatinga, Pantanal, and in the Cerrado of Tocantins. The only previously known record for the Mato Grosso state is more than 50 years old, in a Pantanal area. This paper provides the first record of the species in a Cerrado area of this state, in the municipality of Nova Xavantina, west central Brazil.
Characterization and comparison of acidic polysaccharide populations in Atrina pectinata individuals

GRAPHICAL ABSTRACT ABSTRACT Acidic polysaccharide compositions of individual viscera and adductors of a shellfish species, Atrina pectinate, were characterized by detecting the oligosaccharides from acid hydrolysis using high performance liquid chromatography coupled with mass spectrometry. In total, 6 acidic polysaccharides were found including 2 glycosaminoglycans (GAGs) and 4 non-GAGs, such as chondroitin sulfate and a non-GAG with a →4)-GlcA(1→2)-Man(1→ backbone. As indicated by similarity analysis and multidimensional scaling analysis, acidic polysaccharide compositions of the same shellfish tissue, adductors or viscera, of discrete individuals were similar, while those from different tissues differed significantly.
Validating FTA card skin swabs as a source of DNA from wild amphibians

Amphibians are the most endangered groups of vertebrates, and there is currently an urgent need to implement efficient monitoring schemes based on insights from DNA. However, largely due to their unprotected skin which lacks dead keratinised tissue, current standard techniques for DNA sampling of endangered amphibians are either destructive (sacrifice of entire animals) or can involve distinctly invasive techniques such as tissue sampling based on toe or tail tip clips. The present MSc by Research for the first time quantitatively investigates whether skin swabs with commercially available Whatman FTA cards, a relatively uninvasive technique, can yield DNA samples of sufficient quality and quantity for PCR amplification. In total, swabs from 22 individual great crested newts (Triturus cristatus, the most endangered newt in the UK and an important flagship species for conservation) were analysed, and partly directly compared with toe clip samples. For amplification tests, 7 nuclear microsatellite loci and one mitochondrial locus (ND4) were used; the success rates of PCRs were quantified by replicate PCRs based on DNA extractions using different protocols. While PCR success rates differed across genetic markers, the study showed that, with sufficient replicates, it is possible to efficiently retrieve amplifiable amphibian DNA based on FTA-card skin swabs. The most successful protocol was based on the merging of eight punches from different areas of the FTA card for DNA extraction using the commercially available Qiagen kit, leading to PCR amplification rates which were largely indiscernible from PCRs based on tissue samples. The established new protocol for DNA collection should aid in reducing the invasiveness of DNA collection in future amphibian studies.
Multi-scale First-Principles Modeling of Three-Phase System of Polymer Electrolyte Membrane Fuel Cell

The three-phase system consisting of Nafion, graphite and platinum in the presence of water is studied using molecule dynamics simulation. The force fields describing the molecular interaction between the components in the system are developed to reproduce the energies calculated from density functional theory modeling. The configuration of such complicated three-phase system is predicted through MD simulations. The nanophase-segregation and transport properties are investigated from the equilibrium state. The coverage of the electrolyte on the platinum surface and the dissolution of oxygen are analyzed.
The Insects of Caja de Muertos Island, Puerto Rico

This report is an annotated checklist of 210 species of insects, representing 11 orders and 79 families, which have been recorded for Caja de Muertos, a small island located off the coast of Puerto Rico about 8 miles southeast of Ponce harbor. A brief account is given of the various, mainly entomological, scientific explorations conducted thereon.
Influences of the lateral geniculate nucleus in the specification of primary visual cortex in macaca mulatta

1 Chapter 1: General Introduction.2 Chapter 2: Correlation of lateral geniculate nucleus neuron number to specification of neuron number in normal macaques.15 Introduction.16 Materials and Methods.18 Results.21 Discussion.26 Chapter 3: Effects of prenatal reduction of geniculocortical input on specification of primary visual cortex.30 Introduction.31 Materials and Methods.32 Results.36 Discussion.48
Polyploidy and elevation contribute to opposing latitudinal gradients in diversification and species richness in lady ferns (Athyriaceae)

In ferns, the temperate-tropical sister clades Athyrium and Diplazium present an opportunity to study a latitudinal contrast in diversification dynamics. We generated a taxonomically expanded molecular chronogram and used macroevolutionary models to analyze how diversification rates have changed through time, across lineages, and in concert with changes in elevation and ploidy. We tested a novel model of cladogenetic state-change in which polyploidy can arise as an infraspecific polymorphism, with diversification parameters distinct from those of pure diploids and polyploids. Both Athyrium and Diplazium accelerated their diversification near the Oligocene-Miocene transition. In Diplazium, the rate shift is older, with subsequent net diversification somewhat slower and suggestive of diversity-dependence. In Athyrium, diversification is faster and associated with higher elevations. In both clades, polyploids have the highest rate of net accumulation but lowest (negative) net diversification, while the converse is true for polymorphic species; diploids have low rates of both net accumulation and diversification. Diversification in Athyrium may have responded to ecological opportunities in expanding temperate habitats during the Neogene, especially in mountains, while the pattern in Diplazium suggests saturation in the tropics. Neopolyploids are generated rapidly, primarily through accelerated cladogenesis in polymorphic species, but are evolutionary dead ends.
Spatial heterogeneity in plant-soil feedbacks alters competitive interactions between two grassland plant species

The effects of plants on soil vary greatly between plant species and in mixed plant communities this can lead to spatial variation in plant-soil feedback (PSF) effects. Such spatial effects are thought to influence plant species coexistence, but the empirical evidence for this hypothesis is limited. Here, we investigate how spatial heterogeneity in PSFs influences plant growth and competition. The experiment was carried out with high and low nutrient soils to examine how these effects depend on soil fertility. We collected soil from field plots planted for three years with monocultures of Anthoxanthum odoratum and Centaurea jacea and tested the performance of the two species in a greenhouse experiment in heterogeneous soils consisting of patches of “own” and “foreign” soils and in soils where the “own” and “foreign” soils were mixed homogeneously. In the test phase, plants were grown in monocultures and in 1:1 mixtures in live or sterilized soils. Overall, A. odoratum in monocultures produced less aboveground biomass in heterogeneous soils than in homogeneous soils. Centaurea jacea produced less belowground biomass in live heterogeneous soils than in live homogeneous soils, but there was no difference between sterile heterogeneous and homogeneous soils. The belowground biomass per patch varied more in pots with live heterogeneous soils than in pots with live homogeneous soils for both plant species, but there was no difference between pots with sterile heterogeneous and homogeneous soils. In pots with plant mixtures, the difference in aboveground biomass between the two competing species tended to be smaller in heterogeneous than in homogeneous soils. In pots with heterogeneous soils, both plant species grown in mixtures produced more aboveground biomass in “foreign” soil patches than in “own” soil patches. The responses of plants to heterogeneous PSFs were not different between low and high nutrient soils. Our results show that spatially heterogeneous PSFs can influence plant performance and competition via reducing the growth inequality between the two competing species by allowing selective growth in foreign soil patches, independent of initial soil nutrient availability. Such effect may slow down exclusion processes and thus promote the coexistence of competing species at the local scale in mixed plant communities. A plain language summary is available for this article.
Converting forests to agriculture decreases body size of Carabid assemblages in Zambia

Body size affects both intraspecific and interspecific competition. Land-use affects such interactions within assemblages of species and should, therefore, also change the size structure of these assemblages. In particular one expects a decrease of mean body size with disturbances. We compared interspecific size structure of carabid assemblages between agricultural fields (frequent disturbances) and forests in Zambia using pitfall traps operated across 1 year. Mean body length across species co-occurring within sites in agricultural fields was significantly smaller than in natural forests. Furthermore, in both habitats, we found evidence for ecological clustering in respect to body size, although in forests, body size differences between adjacent-sized species tended to be overdispersed. We also found a positive relationship between log10-transformed body length and log10-transformed activity abundance in forests, suggesting competitive asymmetries between large and small species. Overall, these observations suggest that the size structure of carabid assemblages depends on disturbances as well as competitive interactions. Such interactions seem to be, however, of lower importance within agricultural fields.
Safety of l‐tryptophan technically pure, produced by fermentation with Escherichia coli DSM 25084, KCCM 11132P and SARI12091203 for all animal species based on a dossier submitted by FEFANA Asbl

Abstract In 2015, the EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) issued an opinion on the safety and efficacy of l‐tryptophan produced by fermentation using three strains of Escherichia coli, when used as a nutritional additive for all animal species. The Panel concluded that the safety of l‐tryptophan produced by E. coli SARI12091203 for target animals, consumers, users and the environment could not be assessed because the data submitted did not permit the identity and safety of the strain, and the purity of the additive, to be determined. During the current assessment, the applicant withdrew the application for l‐tryptophan produced by E. coli SARI12091203. l‐Tryptophan produced by E. coli DSM 25084 or KCCM 11132P was considered safe for non‐ruminant target species, the consumer and the environment. For both products, the level of endotoxins and the possible dusting potential indicated a risk by inhalation for the user. In the absence of data, a potential for dermal sensitisation could not be excluded. The Commission gave the applicant the possibility of submitting complementary information to allow the FEEDAP Panel to complete its assessment. The additional data on the characterisation of the additives and on their potential for inhalation toxicity and as skin sensitisers are the subject of the current opinion. Due to improvements in the manufacturing process, the level of endotoxins present in the l‐tryptophan produced by E. coli KCCM 11132P has been markedly reduced; consequently, the endotoxin content does not represent a health risk for the user. The additive has a low acute toxicity by inhalation and is not considered as a potential skin sensitiser. l‐Tryptophan produced by E. coli DSM 25084 is not considered a skin sensitiser. The level of endotoxins in this product, however, represents a risk by inhalation for the user handling the additive.