Miracle-dz/UniFAR-FTUs huggingface dataset:
Surfactant-Enhanced Control of Two Erythroxylum Species by Glyphosate1

Abstract: Glyphosate is the only herbicide used for controlling illicit coca (Erythroxylum coca and E. novogranatense), a source of cocaine. Because commercially available formulations of glyphosate were inconsistent in controlling coca, research was conducted in a large-scale aerial eradication program, greenhouse (in Maryland) and field (Hawaii), to develop more effective control systems. Sixteen surfactants (cationic, nonionic, or mixed) were tested with two commercial glyphosate herbicide formulations, in aqueous or oil-based carrier systems, for coca control. Ultimately, two glyphosate–surfactant systems (COC/OSI-U [a mixture of crop-oil concentrate, Agri-Dex® and organosilicone, Silwet L-77®] and CAT/ANA [cationic surfactant/anionic surfactant, Optima®]) were found that increased glyphosate phytotoxicity fourfold: 1.1 kg ae/ha of glyphosate + surfactant was equivalent to 4.4 kg ae/ha glyphosate without added surfactant, for both species. In consequence, the glyphosate mixture used in Colombia for coca eradication was modified with substantially improved results. Nomenclature: Glyphosate; coca, selected taxa of the genus Erythroxylum, especially E. coca var. coca Lam, E. novogranatense var. novogranatense (Morris) Hieron, E. coca var. ipadu Plowman, and E. novogranatense var. truxillense (Rusby) Plowman. Additional index words: Adjuvants, coca control, herbicide carrier system, herbicide efficacy, narcotic plants, surfactants. Abbreviations: ANA, anionic surfactant; CAT, cationic surfactant; COC, crop-oil concentrate; ECC, E. coca var. coca; ECI, E. coca var. ipadu; ENN, E. novogranatense var. novogranatense; ENT, E. novogranatense var. truxillense; Gly, glyphosate (isopropylamine salt); MSO, methylated seed oil; NIS, nonionic surfactant; OSI, organosilicone surfactant; VO, vegetable oil.
Characterization and potential of a bilayered hydrogel of gellan gum and demineralized bone particles for osteochondral tissue engineering.

Osteochondral (OC) tissue engineering (TE) is a promising strategy to regenerate an acute or degenerative chondral and OC lesions. However, advancing a proper model for the OC is yet on progress. Herein, bilayer hydrogel (BH) based on gellan gum hydrogel (GG) and demineralized bone particles (DBPs) is suggested as a new model. The BH composite can be fabricated easily with a cell-friendly biomaterial and crosslinker. The BH composite was characterized by a morphological method and physicochemical aspect. The mechanical and rheological characters were further confirmed to verify its applicability in the OC TE. Thermodynamic property of the composite was carried out to analyze thermal stability and interaction among matrices. The bioactivity of the material was studied by treating SBF solution for 28 days to examine the formation of crystalline structure in the BH construct. In vitro studies were carried out to study the viability and biochemical characters of the developed biomaterial. In vivo study was performed to analyze biocompatibility of the material and regeneration of the injured OC region implanted with BH composite. The data displayed stable physicochemical properties and mechanical characters when the DBPs were incorporated with a proper amount. The bioactivity of the DBPs loaded hydrogels displayed a high amount of apatite formation. The cytotoxicity of the fabricated material was low which allows application in vitro and in vivo. The biochemical studies displayed a high level of ALP activity and gene expression which shows promising application of DBPs loaded GG in the bone-layer of the BH model. The long-term in vivo study displayed excellent biocompatibility and great potential in the OC defected region. Overall, these results suggest the significance of combined and innovative approaches to improve the therapeutic strategies for OC regeneration and the BH model suggested in this study can be a promising biomaterial model for the OC TE.
Root foraging strategies and nutrient cycling : study on the functional role of the horizontal exploration of soil by plants

Plant nutrition depends on complementary mechanisms : the development of root systems, root uptake and plant ability to control nutrient cycling, e.g. through exudation. The aim of this thesis is to link plant-soil feedbacks involving the cycling of nutrients and root foraging strategies. I first review the different mechanisms of plant influence on nutrient cycling within the soil and assess their respective scales. Considering the direct effect of roots on the soil at the scale of the rhizosphere, I hypothesize that the combination of absorption and exudation may lead to synergies between the roots of a plant. At the scale of the whole root system, I propose a second, heuristic hypothesis: the existence of a trade-off between soil exploration and soil occupation (defined as the ability of plants to influence efficiently nutrient cycling). In a first chapter, I develop a general model of nutrient cycling, to determine under which condition plants should limit the exploration of soil by their roots. I show that limited exploration is an efficient strategy under specific conditions, especially nutrient-poor soils and the existence of synergies between roots. In a second chapter, I characterize soil occupation and nitrogen cycling, by the use of isotopes ratios, in the plant-soil system of three perennial grasses of the savanna of Hwange (Zimbabwe). This field study shows a gradient of root heterogeneity among these grass species. Those showing the more heterogeneous root pattern have a slower but potentially more efficient nitrogen cycling. In a last chapter, I develop a numerical mechanistic model at the rhizosphere scale for a plant taking up phosphorus and increasing its availability through exudation of citrate. I show that, depending on the extent of root influence on soil by exudation and nutrient depletion, competition between roots as well as facilitation arise from the combination of root uptake and exudation. By upscaling rhizosphere processes to the root system, I show that phosphorus losses are minimized by a restricted soil exploration, which backs the hypothesis of a trade-off between soil exploration and occupation. Overall, I developed complementary approaches that took into account several mechanisms and scales of plant-soil interactions. Considering that root functions are not limited to nutrient uptake, but also involve their influence on nutrient cycling, lead to two novel results: the potential existence of intra-plant and inter-root facilitation, and limited soil exploration as an efficient foraging strategy. This work underlines the importance of accurately integrating the mechanisms of plant-soil interaction to assess their nutrient strategies and to predict their impact on nutrient cycling within ecosystems.
(1) Ex ploring T raf ficking GTPase Function by mRNA Expre ssion Profili ng: Use of the SymAtlas We b -Application and the Membrome Datas ets

Despite compl ete sequ encing of the human and mouse g enomes , functional anno tation of nov el gene funct ion still rema ins a majo r challenge in mammali an biology. Eme rging strategi es to help elucidat e unknow n gene function includ e the analysis of tissue ‐ specific pa tterns of mRNA exp ression. A recent study inves tigated the steady ‐ state mRNA express ion profiling of the vast majori ty of pro tein ‐ encoding human a nd mou se genes across a pa nel of 79 human and 61 mouse nonredu ndant tissues. The microar ray data from this study consti tutes the Genom ics Institut e of Novartis Founda tion (GNF ) Hum an and Mouse Gene Atlase s and is publicly avail able for explor ation through the SymA tlas web ‐ app lication (http://sym atlas.gnf .org). We have recent ly rep orted the use of these data and hierarchi cal clusterin g algor ithms to gene rate a global overview of the distribu tion of Rabs , SNA REs, a nd co at machinery componen ts, as well as their respecti ve ad aptors, effe ctors, and regul ators. This systems biol ogy approach led us to prop ose Rab ‐ centr ic protein activi ty hubs as a framework for an integrat ed coding syst em, the membrom e ne twork, which orchestrat es the dynamics of speci alized membran e architec ture of diff erentiated cells. Here, we describe the use of the SymAtlas web‐application and the Membrome datasets to help explore trafficking GTPase function. The human and mouse membrome datasets are available through the Membrome homep age (http://ww w.mem brome.or g/) and correspo nd to subsets of the SymAtlas content restricted to known membrane trafficking components. Considering the fragmentary nature of the current reductionist approaches in elucidating trafficking component functions, the membrome datasets provide a more focused systems biology perspective that not only complements our current understanding of transport in complex tissues but also provides an integrated perspective of Rab activity in controlling membrane architecture.
A Potential 17- β Estradiol degrader Bacterium Isolated from Sewage water

A successful 17 β estradiol (E2) degrading bacterium was isolated from waste water of Saft Elhena drain in Egypt. Molecular identification of the isolated bacteria was carried out using DNA (RAPD), the amplification was made by restriction analysis of amplified 16s rDNA and sequencing. Alos, the bacterium was incubated in saline media under different levels of 17 β-estradiol anaerobically. Levels of CO2 production were examined by GC and residual 17 β-estradiol was tested by HPLC to measure biodegradation capacity. Identification of the genetic element responsible of the gene resistance in the bacteria was tested. The sequence analysis of 16S rRNA gene for 17 β estradiol degrader bacterium showed that its affiliations to phylum Enterobacteriaceae, and it belonged to the genera Klebsiella sp. Results revealed that Klebsilla was cabable of degrading estradiol and that the responsible resistance gene was mostly the chromosomal gene. However, further studies are still going on to locate and examine the gene responsible for E2 resistance.
Fatty Acid Profile Differences Among the Muscle Tissue of Three Rodents (Hydroahoerus hidrochaeris, Cuniculus paca and Cavia porcellus) and one Lagomorph (Oryctolagus cuniculus)

The consumer demand for functional food with nutraceutical properties has increased in recent years, and the food’s fatty acid profile is one of the factors that define its potential value asa functional food. The aim of the present study was to compare fatty acids composition of semitendinosus muscle in two native rodents, the capybara (Hydroahoerus hidrochaeris) and lowland paca (Cuniculus paca) and two domesticated species, one rodent, the guinea pig (Cavia porcellus) and one lagomorph, the common rabbit (Oryctolagus cuniculus). The animals were fed with forage-based diet. The fatty acid composition in lyophilized tissue was determined by gas chromatography. The capybara, lowland paca and guinea pig had the highest levels of omega-3 (n-3) fatty acids, predominantly α-linolenic acid (p<0.05). The guinea pig and common rabbit showed a higher content of linoleic acid (18:2 n-6) (p<0.05). The n-6: n-3 fatty acids ratio was higher to the common rabbit (p<0.05) with 8.9, in contrast, capybara and lowland paca had the lowest ratio, with lower than zero values indicating a predominance of n-3 fatty acids. These results were presented without any diet manipulation. The guinea pig meat contained an adequate balance of n-6 to n-3 fatty acids (< 4) whereas in rabbit meat there was an excess of n-6 fatty acids. The capybara and lowland paca can be considered as sources of n-3 fatty acids, represented by α-linolenic acid (18:3 n-3). These results confirm that native species not subjected to genetic selection and intensive feeding, showed higher content of n-3 fatty acids.
Dirina Paradoxa (Fée) Tehler, the Correct Name For Dirina Approximata Zahlbr

Of Eumitria species found in East Africa (Swinscow & Krog 1974), Usnea baileyi (Stirton) Zahlbr. is sometimes almost as robust but differs in bearing isidia over much of the cortex and also on the pseudocyphellae. Both U. elata Mot. and U. cristata Mot. have angulate branches, the first slightly and the second strongly so, in addition to being isidiate. U.firmula (Stirton) Mot. , a smaller plant, has a distinctly stramineous, not greenish-grey, tinge, and the branches are profusely clothed with rather long fibrils. While U. subcristata Dodge has densely tuberculate branches without isidia, it has a much smaller thallus with a sparse, open system of branching, and it lacks a periaxial pigmented layer. U. liechtensteinii Steiner, though strongly tuberculate, is exclusively saxicolous and has a fastigiate system of branching. Usnea trullifera Nyl. has been reported from East Africa (Motyka 1936-38), but the supporting specimen is presumed lost (in B); the type was from Tahiti and is in BM. Though the branches are strongly tuberculate and lack isidia, the plant is much smaller and is sparsely branched with well-developed fibrils. Both in habit, with its apical apothecia, and in its stramineous colour it is close to U.firmula. None of these species is known to produce psoromic acid, but it must be borne in mind that Usnea species commonly have more than one chemical strain, so that a strain with this chemistry in one of the hitherto known species may await detection. Usnea antiqua is so far known only from Tanzania, where it has been collected at three localities in the West Usambara Mountains at 1600-2000 m alt.
Interleukin-6 (IL-6) and IL-8 Are Induced in Human Oral Epithelial Cells in Response to Exposure to PeriodontopathicEikenella corrodens

ABSTRACT Periodontitis is the inflammatory response in periodontal tissues elicited by bacterial colonization in periodontal pockets. In this response, pocket epithelial cells are the first cells to come into contact with bacteria. To elucidate this mechanism, we determined the adherence of the periodontopathic bacterium Eikenella corrodens 1073, which has a GalNAc-sensitive lectin-like adhesin (EcLS), to a human oral epithelial carcinoma cell line (KB) and the induction of proinflammatory cytokine production in the cells following exposure to this bacterium in vitro. In the adherence assay, EcLS played a role as the adhesin of this bacterium in adherence to KB cells. In a reverse transcriptase PCR, significant interleukin-8 (IL-8) and IL-6 mRNA levels were induced in response to exposure to this bacterium. In an enzyme-linked immunosorbent assay after an 8-h bacterial exposure, the IL-8 and IL-6 protein levels were 13.5- and 8.3-fold higher than those in the nonexposed controls, respectively. These protein responses were time dependent. Interestingly, whenE. corrodens was separated from KB cells by cell culture inserts, a slight stimulation of the IL-6 and IL-8 mRNA and secreted protein levels was seen. These results imply that the direct contact ofE. corrodens 1073 with oral epithelial cells is not necessarily required for the stimulation of IL-6 and IL-8 secretion. We suggest that E. corrodens induces the epithelial cells to secrete proinflammatory cytokines which serve as an early signaling system to host immune and inflammatory cells in underlying connective tissues.
Cloning and Characterization of tdhA, a Locus Encoding a TonB-Dependent Heme Receptor fromHaemophilus ducreyi

ABSTRACT Haemophilus ducreyi is unable to synthesize heme and must acquire it from its only known host, humans. We cloned and sequenced a gene encoding an outer membrane receptor for heme. It was designated tdhA (for TonB-dependent heme receptor A) since it was related by sequence homology to the family of TonB-dependent receptors. TdhA was strikingly similar to open reading frame HI0113 from the genome of Haemophilus influenzae Rd and also shared homology with five other heme receptors, including HxuC, HemR, HmuR, ChuA, and ShuA, from gram-negative bacteria. AnEscherichia coli hemA tonB mutant strongly expressingH. ducreyi tdhA grew on low levels of heme as a source of heme only when an intact H. ducreyi Ton system plasmid was present, formally demonstrating functional TonB dependence.tdhA was expressed poorly in vitro by H. ducreyi and only under conditions of heme limitation. A survey ofH. ducreyi revealed that all tested strains but one synthesized small amounts of TdhA in vitro under heme-limiting conditions. Surprisingly, an isogenic mutant of tdhA as well as its parent, 35000, both required the same high levels of heme for growth (50 μg/ml [77 μM] on agar medium). This result, together with previous findings, suggests that in vitro, the uptake of heme by H. ducreyi is mediated by a TonB- and TdhA-independent mechanism, possibly diffusion.
The Life Cycle of Fasciola hepatica

Fasciolosis is an economically important disease of domestic livestock, in particular cattle and sheep, and occasionally man. The disease is caused by digenean trematodes of the genus Fasciola, commonly referred to as liver flukes. The two species most commonly implicated as the aetiological agents of fasciolosis are F. hepatica and F. gigantica (family Fasciolidae). F. hepatica has a worldwide distribution but predominates in temperate zones while F. gigantica is found on most continents, primarily in tropical regions. The class Trematoda belongs to the phylum Platyhelminthes, and can be divided into two subclasses, the Digenea and Aspidogastrea. The Digenea are characterized by a complex life cycle in which one or more intermediate hosts are involved. Many variations on the life cycle exist, but each typically includes a molluscan primary or intermediate host in which larval multiplication occurs, and a vertebrate final or definitive host in which sexual reproduction occurs. Members of the family Fasciolidae are hermaphroditic and self-fertilization can occur, although sexual reproduction is normally by cross-fertilization in the final host. The story of the discovery of the life cycle of F. hepatica has been recounted before; therefore only a short account will be given here. A list of the principal discoveries is shown in Table 1.1. Integral to the successful completion of the life cycle, the biological factors involved will be discussed in the second part of the chapter. Additional details on many of the aspects of the life cycle will be covered in more depth in subsequent chapters.
Comparison of Bottomless Lift Nets and Breder Traps for Sampling Salt-Marsh Nekton

AbstractVegetated salt-marsh surfaces provide refuge, forage, and spawning habitat for estuarine nekton, yet are threatened by accelerating rates of sea-level rise in southern New England and elsewhere. Nekton responses to ongoing marsh surface changes need to be evaluated with effective and quantitative nekton sampling gear. The goal of this study was to evaluate the effectiveness of different gear for monitoring nekton in emergent salt-marsh vegetation by comparing nekton parameters between Breder traps and bottomless lift nets and between Breder traps made from different materials. Breder traps collected a significantly different nekton community, fewer species, and larger-sized Mummichogs Fundulus heteroclitus than did lift nets. Nekton community composition, richness, and the size of green crabs Carcinus maenas also differed significantly between Breder traps constructed from acrylic and wire mesh. These results show that it is not appropriate to directly compare nekton data between Breder traps and .
The diet of Ophionereis reticulata (Echinodermata: Ophiuroidea) in southeastern Brazil

The ophiuroid Ophionereis reticulata (Say, 1825) occurs in the sediment-rocky shore interface, under small stones. Its diet is analyzed in this short communication. Specimens were collected at the Praia Grande beach, located on the northern coast of the state of Sao Paulo, Brazil, in July, 2002 and January, 2003. The animals were fixed in 70% ethanol and dissected to obtain their stomach contents. Of the total (35), 77.1% (27) had ingested some kind of food and, among those, 81.4% (22) had more than one item. The mean number of food items per stomach was 1.9. Ophionereis reticulata is an omnivorous species, consuming sediment, green and red algae, and polychaetes.
Environmental Characteristics of Nest Sites Selected by Gopher Tortoises (Gopherus polyphemus) in Southern Mississippi

Abstract Nest-site selection can influence both the survivorship of a clutch of eggs as well as the phenotype of resulting hatchlings. The purpose of this study was to determine whether nest sites of Gopherus polyphemus in southern Mississippi differed from randomly chosen prospective nest sites with respect to various habitat parameters. Data were collected that described habitat variables we thought could be biologically relevant. Univariate tests were used to both compare nest sites with non–nest sites, as well as to further narrow the list of variables into those included in an analysis with Akaike's Information Criterion (AIC). Our AIC analysis suggests that the amount of bare soil at the apron and the composition of the soil are important factors when modeling nest-site selection for this tortoise. Aprons with nests contained more bare soil (less vegetation and litter cover) and less clay content in the soil than did randomly chosen aprons that did not have nests. These results indicate that nest sites of G. polyphemus in southern Mississippi differ from random, potential nest sites, implying that females exhibit nest-site selection.
Context‐dependent defence in terrestrial plants: the effects of light and nutrient availability on plant resistance against herbivory

The context‐dependent defence (CDD) hypothesis predicts that defence levels of plant species against herbivory are not fixed but vary with environmental conditions, in a way that is specific for plant species that share evolutionary adaptations to resource conditions exemplified by similar maximum relative growth rates. More specifically, we expected plants from resource‐poor environments to display high defence levels but not when grown under resource‐rich conditions, whereas the reverse – plants from resource‐rich conditions displaying low defence levels but not when grown under resource‐poor conditions – is not necessarily the case. In this study, we used multiple‐choice bioassays in which leaf discs were fed to larvae of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae) as an efficient and effective way of indicating plant defence levels. This generalist herbivore was capable of detecting both inter‐ and intraspecific differences in defence among plant species. The CDD was tested by exploring the effects of various experimental resource conditions (light, nutrients) upon the herbivore preferences and by comparing these preferences with the maximum relative growth rate of plant species. The experimental results provide general support for the CDD hypothesis with respect to nutrient‐level variation but the effects were not related to the origin of the plant species tested. Variation in light conditions did not result in consistent effects upon herbivore preferences. The CDD therefore can be formulated more precisely as: defence levels of plant species vary under different environmental conditions but in a way that is specific for plant species that share evolutionary adaptations to similar nutrient conditions. This more precise CDD hypothesis is a useful addition to existing optimal‐defence theory because of its focus on the possible plastic effects of resource conditions upon plant defence levels. This is relevant when designing experimental plant–herbivore studies.