Miracle-dz/UniFAR-FTUs huggingface dataset:
CHARACTERIZATION OF THE EUKARYOTIC TRANSLATION INITIATION FACTOR 4E (eIF4E) FAMILY MEMBERS IN THE ZEBRAFISH (Danio rerio)

Title of Dissertation: CHARACTERIZATION OF THE EUKARYOTIC TRANSLATION INITIATION FACTOR 4E (eIF4E) FAMILY MEMBERS IN THE ZEBRAFISH (Danio rerio) Kathleen M Gillespie, Doctor of Philosophy 2015 Dissertation directed by: Associate Professor Rosemary Jagus, University of Maryland Center Environmental Sciences The present study examines the six eIF4E cognates in zebrafish. In addition to the prototypical translation initiation factor eIF4E, eukaryotes have evolved eIF4E variants with distinct characteristics, some of which negatively regulate the recruitment of specific mRNAs. Metazoan eIF4E family members fall into three classes, with Class I containing the canonical translation initiation factor eIF4E-1. eIF4E-1 binds eIF4G to initiate translation, a process inhibited by eIF4E binding proteins such as the 4E-BPs and other eIF4E interactive proteins. Analysis of eIF4E sequences from the twenty fish genomes currently available, as well as those of echinoderm, tunicate and cephalocordate, has allowed a glimpse of the origins and evolution of the eIF4E family in vertebrates. All deuterostomes have one representative from each class of eIF4Es. Early deuterostomes such as sea urchins, tunicates, and lancelets have only one from each class; eIF4E-1, eIF4E-2 and eIF4E-3. The distribution of the subclasses of eIF4E-1 is consistent with the duplication of Class I prior to the teleost specific whole genome duplication, probably at one of the whole genome duplications at ~550 (1R) and 500 (2R) mya. Evidence of the duplication of Class I eIF4Es can be seen in elephant shark (Callorhinchus milii), coelacanth (Latimeria chalumnae) and basal ray-finned fish (Lepisosteus oculatus), which have eIF4E-1A, -1B, and -1C. eIF4E-1B has neofunctionalized to become a tissue specific regulator of mRNA recruitment. It has been retained in tetrapods, but lost in higher teleosts. eIF4E-1C, appears to have retained function as a prototypical initiation factor. A duplication of Class II eIF4Es occurred prior to the emergence of the tetrapod branch, becoming eIF4E-2A and -2B. The genes proximal to the eIF4E-2A locus appear to be conserved across teleosts and tetrapods, the eIF4E-2B genetic loci are more variable, suggesting that eIF4E-2A is the ancestral form. eIF4E-2B is retained by amphibians and teleosts, but has been lost in coelacanth and amniotes. Although 88 % identical, eIF4E-2B can be distinguished from eIF4E-2A by its ability to bind trimethyl GTP (TMG) and to complement a S. cerevisiae strain conditionally deficient in eIF4E. This study has shown that duplication within the different classes of eIF4E occurred early in vertebrate evolution with some neofunctionalization, as well as asymmetric losses in different vertebrate classes CHARACTERIZATION OF THE EUKARYOTIC TRANSLATION INITIATION FACTOR 4E (eIF4E) FAMILY MEMBERS IN THE ZEBRAFISH (Danio rerio)
Corn and Sesame Oils Increase Serum γ-Tocopherol Concentrations in Healthy Swedish Women

We studied the effects of dietary intervention with three vegetable oils (Linola, corn or sesame oil, all good sources of gamma-tocopherol) on absolute and relative concentrations of alpha- and gamma-tocopherol in human serum. The oils contained only small amounts of linolenic acid but varying amounts of oleic and linoleic acids, and they had different concentrations of alpha-tocopherol. Forty healthy female students (mean age 26 y) were randomly assigned to one of three groups and consumed a diet that contained one of the three oils for 4 wk. Refined oils were distributed as ingredients in specially prepared buns, in margarine or as dressing. Serum tocopherols, serum lipoproteins and plasma malondialdehyde concentrations were measured. The gamma-tocopherol concentrations normalized to serum lipids increased significantly in the corn and sesame oil groups (P < 0.01), and the alpha-/gamma-tocopherol ratios decreased significantly from baseline concentrations in all groups (P < 0.05). The alpha-tocopherol concentrations did not change during the diet period in any of the three groups. Serum cholesterol, serum apolipoprotein B and plasma malondialdehyde concentrations decreased significantly only in the Linola oil group (P < 0.05). These data show that a moderately modified natural diet that contains both alpha- and gamma-tocopherol increases the serum gamma-tocopherol concentration in healthy women without affecting the serum alpha-tocopherol concentration.
Cell Proliferation Activity in Duct-Ligated Submandibular Gland

Cellular proliferation activity in duct-ligated submandibular glands (SMGs) of rats were evaluated by using index of proliferating cell nuclear antigen (PCNA) immunostaining and 3H-thymidine incorporation. The normal SMGs showed a very low index (<0.1%) of PCNA immunostaining and 3H-thymidine incorporation in the acinar and all the ductal segments. On day 2 and 3 of duct ligation, index of PCNA staining and 3H-thymidine incorporation increased and reached a peak in degranulated granular convoluted tubules (GCTs), duct like structures (DLSs) and dilated excretory ducts (EDs). On day 5 to 10, the glands showed fibrous proliferation around the DLS, and cells in DLSs and dilated EDs had decreasing index of PCNA staining and 3H-thymidine incorporation. On day 14 and 21, the PCNA staining and 3H-thymidine incorporation had decreased and was mainly confined to the DLSs and basal cells of keratinizing epithelial masses. In the unligated SMG of the opposite side of the duct-ligated animals, proliferating cells were found mainly in the acinar compartment from the 2nd to 5th day of ligation.These results suggested that in case of acceleration of secretry function of SMG, secretory cells may proliferate as for the functional adaptation. However, in the case of obstructive lesions of SMG, GCT cells and ductal basal cells may have more potential for proliferation and these cells may be the major participant cells during glandular regeneration and possibly in the histogenesis of the majority of salivary gland tumors, if not all.
A New Invasive Fruit Fly Species from the Bactrocera dorsalis (Hendel) Group Detected in East Africa

Abstract—A new fruit fly species suspected to be from the Bactrocera dorsalis (Hendel) group (originating from Asia), was detected during routine field surveys in the Coast Province of Kenya. Since most species in this group are of tremendous quarantine concern when introduced, and considering the fact that it has never before been detected or reported in continental Africa, surveys were immediately initiated covering a distance of over 3000 km across major fruit-growing and trading localities within Kenya, to determine the extent of spread of the new invasive species. We report on the detection of the flies, preliminary results of the survey, and discuss the potential effects of these flies on the horticulture industry in East Africa. Résumé—Une nouvelle mouche des fruits appartenant vraisemblablement au groupe Bactrocera dorsalis (Hendel) (originaire dTnde), a été trouvée lors d’enquêtes de terrain de routine dans la province côtière du Kenya. Depuis que la plupart des espèces de ce groupe font l’objet de mesure de quarantaine très sévère lors de leur introduction et considérant qu’elle n’a jamais été trouvée ou signalée sur le continent Africain auparavant, une enquête couvrant près de 3000 km à travers les principales localités productrices de fruits du Kenya a immédiatement été lancée afin de déterminer l’aire d’extension de cette nouvelle espèce invasive. Nous présentons des résultats sur la découverte de la mouche ainsi que sur l’enquête, et discutons des effets potentiels de cette mouche sur l’industrie horticole de l’Afrique de l’Est.
Allelopathy among some British grassland species.

Allelopathy, the influence of one plant on another by means of chemical substances, has been extensively studied, and there is now strong evidence that this type of interaction does occur (Whittaker & Feeny 1971; U.S. National Committee for the International Biological Programme 1971; Grodzinsky 1973). Most often investigation of a particular species for possible allelopathic activity has started because of field observations; the species may tend to be surrounded by a bare zone, to have few other species growing beneath it, or in some other way shows an ability to suppress other species which is not expected from its size, density of foliage and other morphological characters. However, the possibility should also be considered that there are other allelopathic interactions where the effects are less extreme, and would not therefore be detected by preliminary field observations, but are nevertheless large enough to alter the balance between species. There are several published reports of species being found to contain toxic materials, when field observations on the species suggest no special toxicity (Welbank 1963; Grant & Sallans 1964; del Moral & Cates 1971). Del Moral & Cates (1971) tested forty species and found toxic materials in every one. All of these studies, however, concerned substances which were extracted from chopped-up plants or which were exuded by dying plant parts; none of them demonstrated the exudation of toxic substances from intact, healthy plants. In many studies of allelopathy the test plants to which the extracts or exudates are applied have been chosen for their convenience rather than their ecological relevance. For example, in the study by del Moral & Cates (1971), the plant volatiles or extracts were applied to seedlings of barley, Bromus tectorum L. and Pseudotsuga menziesii (Mirb.) Franco. Of these three only P. menziesii is native to Washington State, the area from which the donor species originated. The argument implicit in such a choice of convenient species is that all species will respond to the exudates in the same way. This is a very basic assumption and merits investigation. In the research described here, eight species were chosen which give no particular indication, from field observations, that they are involved in allelopathic interactions. The species, four grasses and four dicotyledons, were chosen because they are common in permanent neutral grassland in Britain, and all eight can be found growing together. In order to test whether the exudates have different effects on different species, exudates from each of the eight species were applied to each of the eight, in a factorially arranged experiment. The experiment aimed to study the effects of root exudates from plants young enough to have few dying roots. Leaching from above-ground parts was minimized. There has been little previous work on allelopathy among British grassland species.
Flow-Cytometric Analysis of Testicular Germ Cell Populations in Rams (Ovis Aries)

Flow-Cytometric Analysis of Testicular Germ Cell Populations in Rams (Ovis Aries) The present study was conducted to analyse the germ cell population in testis of rams of different age groups and in wethers by flow cytometric technique and to determine the mitotic index and dihydrotestosterone level in different age groups of rams and in wethers. The germ cells in the testis of all the rams of the different group was analyzed and quantified by flow cytometry after staining with propidium iodide.
Histological study of the atrioventricular node and bundle in the heart of ovine fetus

Summary This study was conducted on the atrioventricular node (AVN) and atrioventricular bundle (AVB) of five four-month-old ovine fetuses. The histological structure of these components was studied by routine histological techniques and use of specific staining methods. The AVN was caudally located adjacent to the root of the aorta. It was almost spherical in shape and consisted of twisty cells. The node was mainly composed of “P” cells. There were not seen internodal pathways in the heart of four-month ovine fetus. The AVB was a direct continuation of the AVN and it passed through the fibrous ring toward the apex of the interventricular septum. At this place the right bundle branch (RBB) was ramified. The cells of the AVB were wider, shorter and lighter than normal myocardial cells. Some of the bundle cells have been changed to purkinje cells, whereas some others still did not represent typical characteristics of purkinje cells.
Early plant recruitment stages set the template for the development of vegetation patterns along a hydrological gradient

Summary Recruitment processes are critical components of a plant's life cycle. However, in comparison with later stages in the plant life cycle (e.g. competition among adults), relatively little is known about their contribution to the regulation of plant species distribution. Particularly, little is known about the individual contributions of the three main recruitment processes – germination, seedling survival and seedling growth – to community assembly, while quantitative information on these contributions is essential for a more mechanistic understanding of the regulation of plant species distribution and biodiversity. Riparian zones along streams provide a globally-relevant case study for evaluating the importance of the different stages of plant recruitment. The natural hydrological gradients of stream riparian zones are currently being restored after a period of world-wide habitat degradation. To identify how recruitment contributes to vegetation patterns and biodiversity in riparian zones, we carried out field experiments at restored lowland streams. We quantified the germination of introduced seeds, and survival and growth of introduced seedlings of 17 riparian plant species across a gradient from the stream channel to upland. The hydrological gradient of riparian zones acted as a strong environmental filter on all three recruitment processes, through imposing an abiotic limitation (excess water) at low elevations and a resource limitation (water shortage) at higher elevations. Other variables, such as soil organic matter content and nutrient availability, only affected recruitment marginally. Species-specific patterns of environmental filtering initiated niche segregation along the riparian gradient during all three recruitment processes, but particularly during germination and seedling growth. These recruitment niches appeared strongly related to indicator values for adult distribution optima, suggesting that at least some riparian plant species may have evolutionary adaptations that promote recruitment under favourable hydrological conditions for adult growth and reproduction. Our results suggest that strong environmental filtering during germination and seedling growth plays an important role in determining later adult distributions, by forming the spatial template on which all subsequent processes operate. In addition to well-known mechanisms, such as competitive exclusion at the adult stage, environmental filtering during early recruitment stages already strongly affect plant distribution and diversity.
The effects of environmental education on children's and parents' knowledge and attitudes towards lemurs in rural Madagascar

Environmental education is widely used to increase awareness of conservation issues. The theory is that increasing knowledge will improve attitudes towards the environment. Often, environmental education is aimed at children with the assumption that this can also impact adults through intergenerational transfer of knowledge and attitudes. However, there are few detailed studies evaluating the effectiveness of environmental education on changing knowledge and attitudes, and whether any changes do transfer between generations. We evaluate the effect of a school‐based education programme run by Malagasy researchers aimed at promoting lemur conservation in Eastern Madagascar. We assess changes in the knowledge and attitudes of participating children and their parents (surveying 126 children and 88 parents across four matched villages, 1 year after two of the villages received environmental education). There was very low awareness of the law protecting lemurs. Attitudes towards lemurs varied between species; with the aye‐aye (considered scary) and the eastern lesser bamboo lemur (considered a pest) being less preferred. Children in villages who received environmental education had higher knowledge about lemurs and more positive attitudes than children in the villages not exposed to the environmental education. Knowledge about lemurs among parents where children had received environmental education was also higher (although not attitudes). Environmental education programmes can have a lasting effect, certainly on knowledge, but engagement of the research and NGO community is needed to build the capacity of teachers in rural areas to enthuse their pupils about ecology and conservation issues.
Landscape factors that shape a slow and persistent aquatic invasion: brown trout in Newfoundland 1883–2010

Aim We investigated watershed‐scale abiotic environmental factors associated with population establishment of one of the ‘world’s 100 worst alien invaders’ on a temperate Atlantic island. Within the context of the conservation implications, we aimed to quantify (1) the early history and demographics (numbers and origins) of human‐mediated brown trout (Salmo trutta) introductions, (2) the current distribution of established populations, and (3) the watershed‐scale environmental factors that may resist or facilitate trout establishment.
Bioavailability of chlorinated dibenzo‐p ‐dioxins and dibenzofurans to dungeness crab (Cancer magister) at marine pulp mill sites in British Columbia, Canada

Synchronous samples of sediment and Dungeness crab (Cancer magister) hepatopancreas, which were obtained for monitoring and assessment purposes at British Columbia, Canada, marine pulp mill sites between 1990 and 1995, were used to calculate biota‐sediment accumulation factors (BSAFs) for individual chlorinated dibenzo‐p ‐dioxin and dibenzofuran congeners (PCDD/Fs). The BSAFs for individual pairs of samples were highly variable, and no systematic trends were apparent in the observed accumulation factors over time, with crab size, with crab lipid concentration, with sediment percent organic carbon, or among mill sites or depositional environments. Composition and source differences in sedimentary PCDD/Fs, which are apparent as principal components analysis class separations in the sediment data set, also did not correlate with differences in BSAFs. This independence from environmental factors provides a valuable endorsement of the BASF concept for the formulation of aquatic effects‐based sediment‐quality criteria and human risk‐assessment guidelines. However, BSAF values did exhibit a significant, nonlinear decrease with increasing log Kow and with sediment and crab PCDD/F concentrations. The correlation between BSAFs and sediment concentrations accounts for between 14 and 81% of the variability in the BSAF values. The PCDD/F congeners that are present in low concentrations and/or have reduced bioavailability are the congeners that have the strongest correlations between the BSAFs and the sediment PCDD/F concentrations. Congeners that are bioavailable to Dungeness crab exhibit poorer correlations between the BSAFs and sediment concentrations.
Auxin, Wounding, and Propagation Medium Affect Rooting Response of Stem Cuttings of Arbutus andrachne

Stem cuttings of Arbutus andrachne L. were taken from basal or terminal portions of branches in October and treated with acid or salt forms of IBA or NAA at several concentrations. Also, the effects of wounding and propagation medium were assessed. Auxin was necessary for root formation, IBA acid being most effective. In general, salt forms of IBA and NAA were less effective than acid forms. Concentration of auxin had a significant effect on rooting regardless of auxin type or chemical form. The greatest rooting percentage, root number, length, and fresh and dry weights were exhibited by basal cuttings treated with 24 m M IBA. Position of the cutting on the branch did not affect rooting except when the IBA acid form was used; basal cuttings were then superior to terminal ones. Wounding, by making two opposite longitudinal incisions at the base of the cutting, increased rooting. The propagation medium had a significant effect on adventitious root formation, which was enhanced with increasing perlite percentage in the medium up to 100%. Chemical names used:1H-indole-3-butyric acid (IBA); α - naphthaleneacetic acid (NAA). Arbutus andrachne is an evergreen tree found in pine and evergreen oak forests in Jordan (Al-Tellawi, 1989). This tree has po- tential use as a landscape plant because of its ornamental features, which include twisted stems and branches, leathery evergreen foli- age, ornamental flowers, decorative fruits, and peeling reddish-brown bark. To introduce this plant into the landscape industry, a feasible propagation method should be developed. Propagation of Arbutus menziesii Pursh. (Hartmann et al., 1990) and Arbutus unedo L. (Stuart, 1979) by stem cuttings is documented. However, to our knowledge, no work has been done on propagation of A. andrachne by stem cuttings. Therefore, the objective of this study was to determine the influence of type, chemi- cal formulation, and concentration of auxin on rooting of A. andrachne stem cuttings taken from two branch positions. The effects of wounding of cutting bases and propagation medium on rooting were also assessed.
Branching out: a remarkable new branching syllid (Annelida) living in a Petrosia sponge (Porifera: Demospongiae)

We describe the morphology and biology of a previously unknown form of branching annelid, Ramisyllis multicaudata gen. et sp. nov., an endosymbiont of shallow-water marine sponges (Petrosia sp., Demospongiae) in northern Australia. It belongs to the polychaete family Syllidae, as does Syllis ramosa McIntosh, 1879, the only other named branching annelid, which was collected from deep-water hexactinellid sponges during the 1875 Challenger expedition. It differs from S. ramosa in parapodial and chaetal morphology. Ramisyllis multicaudata gen. et sp. nov. has segments of several types, including specialized posterior segments on the emergent portions of the worm, and simplified elongate segments that bridge larger cavities in the sponge interior. Aside from the obvious branching form, the new annelid is similar to Parahaplosyllis, differing from it in lacking pharyngeal armature and in the details of the parapodial chaetae and dorsal cirri. Molecular evidence from 16S and 18S rDNA supports a sister-group relationship with Parahaplosyllis, with both being sister to Trypanosyllis and Eurysyllis. The phylogenetic position of R. multicaudata gen. et sp. nov. indicates that branching has evolved independently in Ramisyllis gen. nov. and Syllis. This is supported by differences in the branching process between the two taxa: in S. ramosa branching is initiated by segment addition at the parapodium, whereas in R. multicaudata gen. et sp. nov. segments are added from a region between parapodia. A model for branching in R. multicaudata gen. et sp. nov. is proposed and possible developmental processes underlying branching in Annelida, and body symmetry comparisons with other invertebrates, are also discussed. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164, 481–497.