Miracle-dz/UniFAR-FTUs huggingface dataset:
FUNCTION OF CORE PROMOTERS IN DIFFERENTIAL GENE REGULATION DURING EMBRYOGENESIS

The core promoter is the ultimate target of all transcriptional regulatory processes. The recently discovered diversity of core promoters and basal transcription factors suggests a regulatory role in differential gene expression. However, the direct contribution of the core promoter remains poorly understood. I investigated core promoters and their putative role in differential gene regulation using the zebrafish embryo as an in vivo model system. To analyse the functional requirement for the general transcription factor TATA-box binding protein (TBP), a diverse set of promoters was tested for their TBP dependence. This analysis revealed a differential requirement of TBP for promoter activity. To further explore the roles of core promoters the ability of various core promoters to interact with tissue-specific enhancers was investigated. A high-throughput pipeline combining automated imaging with custom-designed software for registration of spatial reporter gene activity in thousands of zebrafish embryos was developed. The technology was applied in a large-scale screen analysing the tissue specific activities of 202 enhancer - core promoter combinations. A variety of interaction specificities observed suggests an important role of the core promoter in combinatorial gene regulation. Overall, these findings indicate that the core promoter significantly contributes to differential transcriptional regulation in the vertebrate embryo.
Breeding biology of tree swallows in relation to wetland acidity

We examined aspects of the breeding biology of tree swallows (Tachycineta bicolor) in relation to the pH, presence or absence of fish, and dissolved organic carbon concentration in 51 wetlands adjacent to nest boxes northeast of Sudbury, Ontario. Wetland pH was positively related to swallow clutch size, the total volume of eggs in a clutch (clutch volume), the number of fledglings per successful nest, and several measures of nestling size and growth. Swallows breeding near wetlands where fish were present laid earlier, but had smaller eggs and clutch volumes and slower growth of primary feathers than swallows breeding near fishless wetlands. Organic carbon concentrations were poorly related to the reproduction of swallows. These results are discussed in relation to possible mechanisms for the effects of wetland acidity on avian reproduction.
Inoculation with Arbuscular Mycorrhizal Fungi Increases the Yield of Potatoes in a High P Soil

ABSTRACT Arbuscular mycorrhizal (AM) fungi are potentially important tools in agricultural systems that reduce or eliminate chemical inputs common in modem agriculture. We tested the response of potato (Solanum tuberosum L. cv. Superior) to inoculation with AM fungi in a field with very high available P (375 μg g−l soil) in two growing seasons. Inoculation treatments included a commercially available inoculum containing Glomus intraradices, mixed species inocula produced on-farm in mixtures of compost and vermiculite, and a control treatment consisting of a freshly prepared compost and vermiculite mixture. In addition, two farming systems were imposed: conventional chemical fertilizers or dairy manure composted with leaves were applied to meet recommended nutrient requirements. Yields of tubers on a fresh weight basis in the first year were significantly increased by AM fungus inoculum, 33% under conventional fertilizer application and 45% with compost addition vs. controls in each system. The response to inoculation the second year was less; however yields of inoculated plants were 10 to 20% greater than controls. There was a significant positive treatment effect of inoculation upon production of larger sized potatoes in the second year. Neither year saw a marked difference in yield response among AM fungus inocula. These results demonstrate the potential yield benefits of inoculation of potatoes with AM fungi produced on the farm.
Population growth and grain loss of Cathartus quadricollis (Guerin-Meneville) (Coleoptera: Silvanidae) in different stored grains.

1 Department of Agricultural Engineering, Federal University of Viçosa (UFV), Viçosa, MG, 36570-000, Brazil. 2 Department of Animal Biology, Federal University of Viçosa (UFV), Viçosa, MG, 36570-000, Brazil. * Corresponding author. Department of Animal Biology, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil. Phone: +55-31-3899-1919; Fax: +55-31-3899-2537. E-mail address: marco@insecta.ufv. br (MAG Pimentel). Abstract
BLUEBERRY SPANWORM, ITAME ARGILLACEARIA (PACKARD) AND BUMBLE BEE, BOMBUS IMPATIENS (CRESSON) SUSCEPTIBILITY TO NEW BIORATIONAL INSECTICIDES

Biological and cultural control tactics are available for many agricultural pests but insecticides still play an important role in the rapid reduction of pest incidence when damage reaches economic levels. Laboratory and field toxicities of the reduced-risk products spinetoram and flubendiamide to Itame argillacearia (blueberry spanworm) was compared to deltamethrin, a conventional synthetic pyrethroid insecticide. In laboratory experiments, I. argillacearia larvae were highly susceptible to spinetoram and flubendiamide, and efficacy in the field was comparable to that of deltamethrin. Lethal and sublethal effects of the biopesticide formulations of Beauveria bassiana and Bacillus subtilis, and spirotetramat, a new tetramic acid insecticide, to bumble bees, Bombus impatiens, were also assessed. When ingested, field rates of spirotetramat caused high mortality after a week, and B. subtilis significantly reduced drone production. Field rates of spirotetramat, when applied topically, reduced drone production, but drone production varied following topical treatments of either biopesticide.
Helminths in a giraffe ( Giraffa camelopardalis giraffa ) from a zoo in Spain : research communication

A pregnant female Cape giraffe ( Giraffa camelopardalis giraffa ) died from an unknown cause in the Aitana Zoo, Alicante, Spain. Neither clinical signs nor macroscopic lesions were observed at necropsy. The alimentary tract was removed and examined for parasites. A total of 2 724 nematodes were found, including Camelostrongylus mentulatus, Trichostrongylus axei, Ostertagia ostertagi, Teladorsagia circumcincta, Teladorsagia trifurcata, Marshallagia marshalli, Trichostrongylus vitrinus, Trichostrongylus colubriformis, Spiculopteragia asymmetrica and Trichuris giraffae . Only T. giraffae and C. mentulatus have been previously reported from giraffes. The other nematodes are common in mouflons, fallow and red deer, which can usually be found in the same paddock as the giraffes in Aitana Zoo. Although its occurrence is unusual in this host, C. mentulatus was the most abundant nematode in our giraffe. This parasite has been related to disease, and even death, in several wild ruminants.
California's Fading Wildflowers: Lost Legacy and Biological Invasions.

Richard A. Minnich, professor in the Department of Earth Sciences at the University of California, Riverside, has produced a valuable contribution to the growing body of literature attempting to capture the botanical appearance of pre-European California. The book has 5 chapters, 23 figures (maps and photos), 18 data-rich tables, and 14 pages of botanical references, which are a treasure unto themselves. The 5 chapters are arranged chronologically, starting with California’s vegetation in the 16th and 17th centuries and ending with its current vegetation. Minnich tries to make a very strong case that pre-European California was a wildflower paradise and not a bunchgrass prairie. Previous authors, such as Clements (1934) and Heady (1977), argue that pre-European California was dominated by bunchgrasses. But as Minnich points out, this hypothesis was “created by range managers and scientists influenced by the Dust Bowl tragedy of the 1930s, to a point that it became an idée fixe that has kept blinders on us” (page 262). Clements, for example, wrote his 1934 paper during the Dust Bowl era of politics that encouraged government influence on and interference with science. Minnich, now writing over half a century later, states that “the bunchgrass-grazing model is a classic case of too little data and too many ideas” (page 181). However, Minnich is not the first to suggest that bunchgrasses did not dominate the early California landscape. Aptly included in the book is the botanical wisdom and insight of W.L. Jepson and E.C. Twisselmann. Jepson (1925) concluded that much of the Central Val ley of California was dominated by native forbs rather than perennial bunchgrasses. Rancher-botanist Twisselmann (1967) asserted that bunchgrasses were never a prominent component of California’s vegetative cover and rejected the bunchgrass idea based on climate. Minnich quotes Twisselmann’s A Flora of Kern County, California (1967:91–92) on page 174:
Seascape and its effect on migratory life‐history strategy influences gene flow among coastal brown trout (Salmo trutta) populations in the English Channel

Most animal species live in spatially and temporally heterogeneous landscapes where resources are unevenly distributed. Consequently, individuals must adapt their migratory behaviour to optimize feeding and breeding opportunities. Here, we assess the role of life‐history (anadromy) and seascape (a derivation of the concept of landscape) heterogeneity on the genetic connectivity of coastal brown trout populations (Salmo trutta L., 1758).
Some microbiological and chemical properties of Pastirma produced using potassium nitrate and starter culture

In this study, pastirma samples were produced using potassium nitrate and commercial starter culture (Staphylococcus carnosus + Lactobacillus pentosus). The meat for pastirma was dry cured with NaCl, glucose and saccarose together with KNO3. The use of starter culture in pastirma production had a significant effect on counts of total aerobic mesophilic bacteria, Micrococcus/Staphylococcus and lactic acid bacteria. The maximum counts of microorganisms were found in the 2nd stage of the drying process. There was no significant difference between yeast mould counts in control and starter added samples. Nitrite and nitrate residues were lower in commercial starter added samples than in the control group. In addition, starter added samples contained more non-protein nitrogen.
FcγRIII-Mediated Production of TNF-α Induces Immune Complex Alveolitis Independently of CXC Chemokine Generation1

We recently demonstrated a codominant role of C5aR and FcγRIII in the initiation of IgG immune complex-mediated inflammation in mice. In this study, we investigated the relative contribution of FcγRIII in the generation of several cytokines during experimental hypersensitivity pneumonitis/alveolitis in vivo. Induction of immune complex-alveolitis in C57BL/6 mice resulted in strong accumulation of neutrophils into the lung and enhanced chemotactic activity within bronchoalveolar lavage fluid accompanied by an increased production of the proinflammatory cytokines TNF-α and IL-1β as well as the ELR-CXC chemokines macrophage inflammatory protein-2 (MIP-2) and cytokine-induced neutrophil chemoattractant (KC). FcγRIII-deficient C57BL/6 mice (FcγRIII−/−) showed a marked reduction of the inflammatory response due to decreased production of TNF-α, IL-1β, and MIP-2. Results obtained in C57BL/6 mice either lacking the TNF-α class I receptor (TNF-αRI−/−) or treated with neutralizing anti-TNF-α mAb demonstrated an essential contribution of TNF-α for mediating IL-1β release, neutrophil influx, and hemorrhage. Surprisingly, MIP-2 and KC chemokine levels remained largely unaffected in TNF-αRI−/− mice or after functional inhibition of TNF-α. These data suggest that in immune complex alveolitis, the activation of FcγRIII may induce divergent downstream effector pathways with TNF-α acting independently of CXC chemokines to trigger the inflammatory response in C57BL/6 mice.
The ability of synthetic sex pheromone traps to forecast Plutella xylostella infestations depends on survival of immature stages

The potential for using synthetic sex pheromone traps as a simple and practical method of monitoring population densities of insect pests has been investigated in many crop systems. Yet, factors enabling the forecast of infestations based on pheromone trap catches are not fully understood. This study tested the prediction that high survival of immature stages of the target pest is a pre‐requisite for trap catches to correlate well with future infestations on the crop. The influence of parasitoids, as an important natural mortality factor of diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), larvae and pupae in South Africa, on the ability of pheromone traps to forecast infestations was investigated continuously at weekly intervals over 6 years on unsprayed cabbage. During late October–May, when parasitism levels were high (≥50%), infestations and trap catches were significantly lower than during low parasitism (<50%) observed during June–early October. Because infestations were negatively related to parasitism level, trap catches correlated with infestations better when observations were made in the same week during periods of high parasitism. Conversely, when survival of P. xylostella immature stages was high due to low parasitism levels, trap catches correlated with future infestations well for up to 2 weeks. Thus, trap catches can be used to forecast infestations during September–October, a period that coincides with high P. xylostella infestations as a consequence of low natural control by parasitoids. This is the first study to show that the ability of pheromone trap catches to forecast infestations depends on survival of the immature stages of the target pest.
Analysis of RNA interference in the parasitic nematode Haemonchus contortus

Parasitic nematode infections worldwide cause a significant impact on human health, as well as economic and welfare losses to the animal and agriculture industries. The principal method of control for parasitic nematode infections is currently limited to repeated treatments with anthelmintic drugs, but widespread resistance to all major classes of these drugs is a growing problem. As a result, there is an urgent need for alternative methods of controlling these infections, and the development of molecular vaccines and novel drugs represent two possible approaches. However, both these approaches require a deeper understanding of gene function in order to identify suitable control targets. This project examines RNA interference (RNAi) in the parasitic nematode Haemonchus contortus to determine if this could be developed as a functional tool and advance the discovery of novel control targets for parasitic nematodes. RNAi has proven less effective in parasitic nematodes than in the free-living model nematode Caenorhabditis elegans and it is unclear why this is so. This project examined the reliability of RNAi in H. contortus, and several genes were successfully silenced using RNAi. Further analysis of RNAi susceptible genes revealed that RNAi silencing appears to be related to the site of expression of the target gene; genes expressed in tissues which are accessible to the environment such as intestine, excretory cell and amphids were silenced by RNAi. Upstream promoter regions of RNAi susceptible genes were examined for the presence of motifs which may regulate spatial gene expression, an approach that could be used to predict gene susceptibility to RNAi. RNAi treated larvae were subsequently used to infect sheep in the first in vivo RNAi study, resulting in a significant impact on worm survival in vivo. In addition, several components of the RNAi pathway in H. contortus were characterised in this project, demonstrating the presence of a functional RNAi pathway that is capable of reliably silencing genes. In conclusion, the findings presented in this project suggest that RNAi may be used in the future to evaluate the function of a novel vaccine or drug target for controlling H. contortus infections in sheep.
Low MHC variation in the polar bear: implications in the face of Arctic warming?

Animals in the Arctic have low pathogen diversity but with rapid climate warming, this is expected to change. One insidious consequence of climate change is exposure of Arctic species to new pathogens derived from more southern species expanding their range northward. To assess potential vulnerability of polar bears to disease exposure, we examined genetic variation in major histocompatibility complex (MHC) loci (part of immune system) in Canadian polar bears and found low genetic diversity, consistent with long‐standing exposure to low pathogen/parasite loads. All polar bears surveyed showed maximum linkage disequilibrium between DRB/DQB loci and 12% of individuals had a duplicated DQB gene haplotype. These results may reflect balancing selection at these loci, a response to an earlier immune‐challenge and/or be artifacts of polar bear‐brown bear divergence. Consistent with the latter, we found one DQA allele in polar bears that was also a brown bear DQA allele. The reported low MHC diversity and high linkage disequilibrium may have serious implications for polar bear resistance to new pathogens, which would be maladaptive to species in an environment undergoing rapid climate change, such as the Arctic.
Effects of Girdling and Leaf Removal on Fruit Set and Vegetative Growth in Grape

The effect of the carbohydrate supply on fruit set and on the development of the inflorescence, from flowering to three weeks after flowering, was investigated using field-grown Sauvignon blanc grapevines (Vitis vinifera L.). Carbohydrate supply in individual shoots was manipulated by leaf removal and by isolating them from the parent vine using a steam girdle at their bases. Shoots were either not girdled and had no leaves removed (control) or girdled with 0, 1, 2, 4, 6, 8, 10, or 12 leaves removed. The fresh and dry weight of each remaining leaf and internode were used as indicators of carbohydrate supply. Effects of carbohydrate supply on reproductive growth were assessed by recording the dimensions and fresh and dry weights of the rachis and berries. Percentage fruit set was determined from flower and berry counts. Fruit set and vegetative growth responded in an exponential and linear manner, respectively, to changes in carbohydrate supply. Elevated carbohydrate supply increased fruit set to 55% compared with 33% in the controls. There was no fruit set in the harshest treatments which had 10 or 12 leaves removed. Removing only one or two basal leaves substantially reduced fruit set, although up to four leaves had to be removed before the dry matter accumulation in the basal part of the shoot declined to levels similar to those in the ungirdled control. The reduction in fruit set, despite an apparent increase in available carbohydrates, indicates the importance of the adjacent basal leaves to the developing cluster. The wide range of fruit sets achieved in this experiment, and their exponential responses to carbohydrate supply, indicate that carbohydrate is the major determinant of fruit set in grapes. Moreover, symptoms such as abortion of branches of the rachis and similar to those of the disorder early bunchstem necrosis (EBSN) increased as the level of carbohydrate supply declined. This indicates that EBSN can be caused by inadequate carbohydrate supply, and is not necessarily related to problems of nitrogen nutrition or of mineral imbalance.
Interruptions of terrestrial feeding as a way to decrease the non-digestible fraction of the bolus: field observations and laboratory experiments in Mallard

Dabbling ducks commonly feed on land, especially in agricultural environments. During field observations in western France, wintering Mallards Anas platyrhynchos were observed to interrupt terrestrial feeding regularly and go to the water. Laboratory experiments show that feeding interruptions occur when food is mixed with non-digestible material, and that water is used to filter this indigestible bulk. When filtering is impossible because of water deprivation, the ingestion of non-digestible material reduces the 24 hour intake of wheat in the laboratory. Terrestrial feeding interruptions have important costs, feeding sessions increased in length when ducks fed farther from water. Since the birds need water, and interruptions have a cost, only a fringe of vegetation around the water-bodies is used by terrestrial foraging Mallards. These results clarify our understanding of the cause of this behaviour in Mallards, and may have implication for the design of nature reserves.
TRIPS (THYSANOPTERA) ASOCIADOS A AGALLAS DE Ficus benjamina (LINNAEUS, 1767) (MORACEAE) EN LA REGIÓN CENTRAL DE COLOMBIA

En Colombia han sido utilizados ampliamente arboles de Ficus benjamina como ornamentales en zonas verdes urbanas. En los ultimos anos, se ha observado en estas plantas un incremento en los sintomas de ataque de trips (hojas plegadas y necrosadas); pero a pesar de ello, es poco lo que se conoce sobre las especies que se encuentran presentes. Por esta razon, se realizo un reconocimiento de la entomofauna en varias ciudades del pais, encontrando las especies de trips Gynaikothrips garitacambroneroi Retana, 2006 (fitofago) y Androthrips ramachandrai Karny, 1896 (depredador), ambas reportadas por primera vez para Colombia. Adicionalmente, se recolecto el chinche depredador Montandoniola moraguesi (Puton) asociado a estas agallas. Se presentan las diagnosis de las dos especies de trips apoyadas en fotografias de microscopia electronica, con el animo de mostrar en detalle la morfologia de estos insectos.
Assessment of possible association between rs378854 and prostate cancer risk in the Serbian population

Prostate cancer (PCa) is the second most commonly diagnosed cancer among men worldwide. Despite its high incidence rate, the molecular basis of PCa onset and its progression remains little understood. Genome-wide association studies (GWAS) have greatly contributed to the identification of single nucleotide polymorphisms (SNP) associated with PCa risk. Several GWAS identified 8q24 as one of the most significant PCa-associated regions. The aim of this study was to evaluate the association of SNP rs378854 at 8q24 with PCa risk in the Serbian population. The study population included 261 individuals diagnosed with PCa, 257 individuals diagnosed with benign prostatic hyperplasia (BPH) and 106 healthy controls. Data quality analysis yielded results showing deviations from Hardy-Weinberg equilibrium in groups of PCa patients and BPH patients as well as in the control group. There was no significant association between alleles and genotypes of the genetic variant rs378854 and PCa risk in the Serbian population. [Projekat Ministarstva nauke Republike Srbije, br. 173016]
BIOLOGÍA FLORAL Y REPRODUCTIVA DE LA GULUPA PASSIFLORA EDULIS SIMS F. EDULIS

Se estudio la biologia floral y reproductiva de Passiflora edulis f. edulis en cultivos ubicados en la Cordillera Oriental en los Andes colombianos (Buenavista, Boyaca). La flor presento antesis entre las 6 y las 8 hrs, la longevidad floral promedio fue de 25 hrs. Se reconocieron cuatro fases fenologicas: (1) Femenina con hercogamia (2) Homogama con hercogamia (3) Homogama sin hercogamia y (4) Senescente. Aunque el estigma esta receptivo durante todas las fases florales, se obtuvo mayor produccion de frutos en las fases segunda y tercera. La donacion del polen, en su mayoria ocurrio en la fase dos con una viabilidad del 96%. El nectar mostro una tendencia ascendente durante la vida floral. Los experimentos de polinizacion indican que la gulupa es una variedad altamente autocompatible, pero requiere de los polinizadores para producir una buena cosecha, pues solo el 33% de los frutos se forma sin el acceso de estos. Los resultados sugieren que la gulupa tiene una estrategia floral mixta con el potencial para promover endogamia y entrecruzamiento genetico, y que la conservacion de las abejas polinizadoras es crucial en la productividad de este frutal.