Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and characterization of a novel repressor site in the human tumor necrosis factor α gene

In human monocytic cell lines, tumor necrosis factor alpha (TNF alpha) expression is induced by phorbol myristate acetate (PMA). We have identified positive and negative cis-acting elements in the TNF alpha promoter by deletion analysis. Here we present the initial characterization of the repressor element. The repressor element was shown to function in either orientation and at various distances upstream from the positive element of the TNF alpha promoter. The TNF alpha repressor site (TRS) has been localized to a 25 bp region between base pairs -254 and -230 in the promoter. This region contains a 10 bp sequence with homology to the binding site of the activator protein AP-2. Mutation of the 6 C's of this 10 bp AP-2-like site abolish TRS repressor function. However, this AP-2-like site is not a binding site for AP-2 protein based on gel retardation analysis. In addition, a well-characterized AP-2-binding site placed upstream of the positive element of the TNF alpha gene did not cause repression. Therefore, this repression is very likely mediated by a novel protein(s) which interacts with the AP-2 consensus site in the TRS.
Gait transition speed, pectoral fin-beat frequency and amplitude in Cymatogaster aggregata, Embiotoca lateralis and Damalichthys vacca

Surfperches are labriform swimmers and swim primarily with their pectoral fins, using the tail to assist only at higher speeds. The transition, from pectoral to pectoral and caudal fins, occurs at a threshold speed that has been termed physiologically and biomechanically 'equivalent' for fishes of different size. The gait transition (U p-c ) of Cymatogaster aggregata occurred at a higher speed (measured in bodylengths s -1 ) for smaller fish than larger fish. At U p-c , pectoral fin-beat frequency was size-dependent: smaller fish have a higher pectoral fin-beat frequency than larger fish. In contrast, at low speeds (i.e. <60% of U p-c ) the pectoral fin-beat frequency was independent of the size of the fish. Inter-specific comparisons of U p-c , pectoral fin-beat frequency and amplitude among C. aggregata, Embiotoca lateralis and Damalichthys vacca showed that C. aggregata had a higher U p-c than E. lateralis and D. vacca. The pectoral fin-beat frequency at U p-c showed no significant differences among species. Cymatogaster aggregata achieved higher U p-c , in part, through increased fin beat amplitude rather than frequency. These differences in performance may be related to the different habitats in which these species live.
Molecular Phylogenetic Analysis of Relationships of the Tropical Salamander Genera Oedipina and Nototriton, with Descriptions of a New Genus and Three New Species

Abstract Sequences of two mitochondrial genes (385 base pairs of cytochrome b and approximately 520 base pairs of 16S DNA) were gathered for 26 taxa of the Middle American plethodontid salamander genera Nototriton and Oedipina and from three outgroup members of the tribe Bolitoglossini. Phylogenetic analyses of these data reveal well-supported cladistic structure and demonstrate the paraphyly of the moss salamanders of the genus Nototriton, which includes two well-defined clades. One clade, the sister taxon of Oedipina, corresponding to the Costa Rican and Honduran species of the picadoi, richardi, and barbouri groups, retains the name Nototriton. A new name is required for the second clade, the sister taxon of Oedipina plus Nototriton (sensu stricto). This clade, which we name Cryptotriton, is well supported morphologically and includes the species of the nasalis and adelos groups. A new species of Nototriton from Monteverde, Costa Rica, is described as Nototriton gamezi. Species of Oedipina fall into two clades that we treat as subgenera. Oedipina (sensu stricto) includes the longer-bodied, generally more slender and darker colored species and is the more speciose clade. Oedopinola includes the shorter-bodied, generally more robust and lighter-colored species. Two new species of the latter clade are described, Oedipina maritima from the lowlands of northwestern Panamá, and Oedipina savagei, from uplands of southwestern Costa Rica.
Geographic Variation of Paddlefish Allozymes and Mitochondrial DNA

Abstract North American paddlefish Polyodon spathula historically occurred in the Mississippi, Saint Lawrence, and Alabama rivers, as well as several other Gulf of Mexico coastal drainages. Recent population declines in some locations and the local extirpations of others purportedly have been due to habitat loss, overharvest, and other biotic and abiotic changes to riverine ecosystems. Mitigation for these declines has emphasized hatchery production and supplemental stocking programs, which use a number of geographical sources for parental stock. To investigate phylogeographic relationships within and among several watersheds, we surveyed allozyme and mtDNA variation among 189 individuals collected from six regions of the Mississippi River drainage plus the Mobile Bay and Pearl River drainages. Paddlefish exhibited lower levels of allelic and haplotypic diversity than other freshwater species, a characteristic shared with other “primitive” fishes. Allozyme variation at 64 presumptive loci was segregated i.
Border-ownership computation reflecting consistency of surface properties

References Kogo, N. , Strecha, C. , Van Gool, L. , and Wagemans, J. (2010). Surface construction by a 2-D differentiation-integration process: A neurocomputational model for perceived border ownership, depth, and lightness in Kanizsa figures. Psychol. Rev. 117, 406–439. Peterson, M.A., and Salvagio, E. (2008). Inhibitory competition in figure-ground perception: context and convexity. J. Vis. 8, 4.1–13. Yin, C. , Kellman, P.J., and Shipley, T.F. (1997). Surface completion complements boundary interpolation in the visual integration of partly occluded objects. Perception 26, 1459–1479. Zhaoping, L. (2005). Border ownership from intracortical interactions in visual area V2. Neuron 47, 143–153. Zhou, H. , Friedman, H.S. , and von der Heydt, R. (2000). Coding of border ownership in monkey visual cortex. J. Neurosci. 20, 6594–6611. Cown C’own
Game Parks before and after Lewis and Clark: Reply to Lyman and Wolverton

Data from historic accounts (Kay 1994, 1998; Boyd 1999; Martin & Szuter 1999 a , 1999 b ), late Quaternary environments (Mehringer 1996), and zooarchaeology (Lyman & Wolverton 2002 [this issue]) have potential value in conservation biology. Both historic accounts and the fossil record help biologists evaluate those regions potentially suitable for the establishment of certain species of large animals. At stake are fresh interpretations of what regulated the abundance and scarcity of big game that survived late-Pleistocene extinctions. In the Great Plains and Northwest of the United States the distribution and abundance of megafauna covaried not only with habitat quality but also with human predation (Martin & Szuter 1999 a , 1999 b ). Captain William Clark recognized this when he wrote (on 29 August 1806; Lewis & Clark 1893): “With regard to game in general, we observe that the greatest quantities of wild animals are usually found in the country lying between two nations at war. ” We view humans, “the ultimate keystone species” (Kay 1994), as a crucial variable influencing the range of terrestrial megafauna at any time, past and present. We sketch two designs for parks or reserves based on historical documents and the prehistoric fossil record. We depart from Lyman & Wolverton (2002, this issue) in interpreting the meaning of the dramatic shifts in numbers of game observed by Lewis and Clark.
Antimicrobial peptides: a review of how peptide structure impacts antimicrobial activity

Antimicrobial peptides (AMPs) have been discovered in insects, mammals, reptiles, and plants to protect against microbial infection. Many of these peptides have been isolated and studied exhaustively to decipher the molecular mechanisms that impart protection against infectious bacteria, fungi, and viruses. Unfortunately, the molecular mechanisms are still being debated within the scientific community but valuable clues have been obtained through structure/function relationship studies1. Biophysical studies have revealed that cecropins, isolated from insects and pigs, exhibit random structure in solution but undergo a conformational change to an amphipathic α-helix upon interaction with a membrane surface2. The lack of secondary structure in solution results in an extremely durable peptide able to survive exposure to high temperatures, organic solvents and incorporation into fibers and films without compromising antibacterial activity. Studies to better understand the antimicrobial action of cecropins and other AMPs have provided insight into the importance of peptide sequence and structure in antimicrobial activities. Therefore, enhancing our knowledge of how peptide structure imparts function may result in customized peptide sequences tailored for specific applications such as targeted cell delivery systems, novel antibiotics and food preservation additives. This review will summarize the current state of knowledge with respect to cell binding and antimicrobial activity of AMPs focusing primarily upon cecropins.
ARTIFICIAL DIET FOR MASS PRODUCTION OF THE CODLING MOTH, CARPOCAPSA POMONELLA (LEPIDOPTERA: OLETHREUTIDAE)

Abstract An artificial diet for rearing the codling moth is described. It is a modification of a casein–wheat germ diet that was initially developed for the cabbage looper. Agar was replaced by a mixture of wood sawdust, wheat flour, and wood pulp. Growth of microorganisms was controlled by sorbic acid and aureomycin, and by lowering the pH of the diet to 3.5 with citric acid. Production cost for dietary ingredients was about $1/1000 moths. The moths were slightly smaller than those reared on apple. When confined in cages, the sterilized diet-reared moths were somewhat less competitive than the apple-reared insects. However, sterilized diet-reared male moths released in an apple orchard dispersed more rapidly than sterilized apple-reared males.
Changes in Essential Oil Content and Composition of Catnip (Nepeta cataria L.) During Different Developmental Stages

Abstract The variations in content and compositions of catnip (Nepeta cataria) essential oil were examined at different developmental stages (i.e. vegetative, floral budding, full flowering, and fruit set). The essential oil of the plant was extracted by hydrodistillation. The yield of essential oils (w/w %) were 0.3, 0.5, 0.9, and 0.4 % at vegetative, floral budding, full flowering, and fruit set stages, respectively. The essential oils were analyzed by GC and GC-MS. A total of 13, 12, 14, and 11 components were identified and quantified at the above mentioned stages, respectively. The essential oil content showed significant increase at full flowering stage. Three components, 4a-α,7-α,7a-β-nepetalactone (55 - 59 %), 4a-α,7-β,7a-α-nepetalactone (30 - 31.2 %), and α-pinene (2.7 - 4.6%) were the major oil constituents of all growth stages. The proportions of 4a-α,7-α,7a-β-nepetalactone and α4a-α,7-β,7a-α-nepetalactone, as major oil constituents were highest at fruit set and full flowering stages, respectively.
Evaluation and characterization of a novel probiotic Lactobacillus pentosus PL11 isolated from Japanese eel (Anguilla japonica) for its use in aquaculture

In the present study, a potential Lactobacilli probiotics were isolated from Japanese eels (Anguilla japonica) and characterized and evaluated for their possible use in eel farming. Sixteen Lactobacilli were isolated from intestines of Japanese eels, using selective media. The lactobacilli strains (represented as PL1 to PL16) were screened by their ability to produce digestive enzyme. Among these, three strains (PL11, PL13 and PL16) producing four digestive enzymes (amylase, cellulase, protease and phytase) simultaneously were characterized further using API ZYM kit. From these, PL11 (Lactobacillu (L.) pentosus) was identified as potential probiotics candidate producing 15 enzymes among 20 tested. Further examination of biological activities of PL11 revealed tolerance against pH, artificial bile juice and antibacterial activity against several fish pathogenic bacteria. The in vitro competitive exclusion assay also revealed 88.4% reduction in adhesion of fish pathogen (Edwardsiella tarda) by PL11 to host intestinal mucus. In vitro incubation of Japanese eel foregut with Baclight-labelled PL11 showed colonization of the enterocyte surface by confocal and scanning electron microscopy. In summary, PL11 isolated from eels could serve as a potential probiotics with acid and bile tolerance, production of digestive enzymes, antibacterial activity and inhibition of fish pathogen adhesion to intestinal mucus.
Identification of QTLs for domestication‐related and agronomic traits in an Oryza sativa×O. rufipogon BC1F7 population

Asian cultivated rice was domesticated from the wild rice, Oryza rufipogon and throughout the domestication process, a wide range of morphological and physiological changes altered the ancestral form. This study was conducted to identify the genetic basis of changes associated with the domestication process. An recombinant inbred line (RIL) population consisting of 120 lines was developed from a cross between the japonica cultivar, 'Hwayeongbyeo' and a presumed wild progenitor, O. rufipogon Griff. Acc.01944. The population was genotyped with 124 simple sequence length repeat (SSR) markers, providing an average interval size of 15 cM, and also evaluated for 20 traits related to domestication and agricultural performance. A total of 63 quantitative trait locus (QTLs) and one locus associated with qualitative variation for pericarp coloration were identified using single point and composite interval analysis. The number of QTLs per trait ranged from one to seven. Phenotypic variation associated with each QTL ranged from 3.7 to 40.4%, with an average of 15.3%. The results indicated that most domestication-related traits clustered in chromosomal blocks, and the positions of many of these clusters were consistent with those reported in previous studies and with skewed segregation ratios in these BC 1 F 7 RILs. For 13 (20.6%) of the QTLs identified in this study, the O. rufipogon-derived allele contributed a desirable agronomic effect despite the overall undesirable characteristics of the wild phenotype. Favourable alleles from O. rufipogon were detected for panicle length, spikelets per panicle, days to heading and leaf discoloration associated with cold stress. When compared with previous studies involving interspecific crosses, it can be concluded that 0. rufipogon is useful as a source of valuable alleles for rice improvement and that many of the introgressed regions contain genes that have a favourable impact on phenotype in different genetic backgrounds and different environments.
Effect of Cannabis sativa L. Seed (Hempseed) on Serum Lipid and Protein Profiles of Rat

Cannabis sativa L. is considered as nutritional plant. Whole hempseed typically contains over 30% oil (3%saturated and 28%unsaturated fatty acids) and about 25% protein. This study was conducted to evaluate the effect of hempseed on lipid and protein profiles of rats. After the acclimatization, at the beginning of experiment (day 1) the feeding of animal stopped and after 12hr fasting the animal anesthetized by ketamine/xylazine combination and 2ml blood of heart was taken. The rats had free access to normal diet and hempseed for 20 days and at the end of experiment (day 20) blood was taken again. The blood parameters were measured by automated biochemical analyzer. Hempseed significantly (p=0.004) decreased the mean fasting serum LDL level and also significantly increased the mean fasting serum HDL and total protein levels (p=0.01). The mean fasting triglyceride, total cholesterol and albumin levels didn't significantly change. The significant level was 0.05 or less. Short term hempseed feeding has improved blood lipid and protein profile. In the light of this research, it is recommended that individuals who have high cholesterol and LDL levels or affected to coronary artery diseases (CAD) and liver diseases, they can use hempseed variety that cultivated in Khorasan province of Iran in their food preparation.
DIFFERENTIAL LIFE HISTORY PHASE EXPRESSION IN TWO COEXISTING SPECIES OF SCYTOSIPHON (PHAEOPHYCEAE) IN NORTHERN CHILE 1

The identity of two phaeophycean taxa that monopolized the middle‐lower rocky intertidal zone of a coastal area chronically exposed to copper mine wastes in northern Chile was unraveled. One of them was preliminarily identified as the gametophytic stage of Scytosiphon lomentaria (Lyngbye) Link. The other, a dark crust, resembled the alternate stage of some Scytosiphon species. Comparative analysis of morphology, life history, and DNA sequences strongly suggests that crusts corresponded to sporophytic S. tenellus Kogame and confirm that erect thalli belonged to S. lomentaria. A clear segregation of erect and crustose thalli was found using internal transcribed spacer region 1 and RUBISCO spacer sequences. Furthermore, whereas crusts always grouped with S. tenellus, erect thalli always grouped with S. lomentaria. Life history studies failed to connect the two entities. First, field‐collected S. tenellus produced progeny that either recycled the crust, which reproduced by unilocular zoidangia, or developed into erect thalli. The latter, unlike typical gametophytic S. lomentaria, developed patchy sori of plurilocular zoidangia. Second, S. lomentaria displayed a direct‐type life cycle, in which progeny from erect individuals only developed into erect thalli and produced only plurilocular zoidangia. This constitutes the first experimental study on Scytosiphon from the Pacific coast of South America and the first report of S. tenellus on this coast. It is also the first report of the crustose stage of Scytosiphon appearing as a perennial and dominant algal species in a temperate rocky intertidal system.
Influence of patch plant density on herbivory levels by Etiella zinckenella (Lepidoptera: Pyralidae) on Glycine max and Crotalaria pallida.

Experiments were conducted to determine the influence of the density and size of patches of soybeans ( Glycine max (L.)) on the extent of pod damage by the lima bean pod-borer Etiella zinckenella (Treitschke). In addition, an evaluation was made of changes in rates of parasitism as a function of changes in patch characteristics. Low-density plots had a greater proportion of pod damage than did high-density plots. Plot size did not influence the proportion of pods attacked per plant. Larval parasitoids of E. zinckenella , in general, were not influenced by plant density but were influenced by host herbivore density. Other experiments were conducted to determine if mixtures of soybeans with a feral host, Crotalaria pallida Ait, a species in the Fabaceae, would influence damage by the pod borer or parasitism. No differences were observed between mixed species plots and pure C. pallida or pure soybean plots, in the number of E. zinckenella larvae per plant raceme nor in the level of parasitism. The abundance of pods produced by plants as a function of cultivar type, patch characteristics and time of season were also recorded.
Sapwood/Heartwood Width Relationships with Tree Age in Balsam Fir

On the basis of five response variables, the sapwood/heartwood relationships with tree age were studied in balsam fir [Abies balsamea (L.) Mill. ] trees. One hundred and one samples, from a wide range of stand densities, were collected from the university forest near Thunder Bay, Ontario. The age at breast height ranged from 4 to 85 years. The five response variables measured were the number of sapwood and heartwood rings, sapwood and heartwood width and sapwood basal area. First and second degree polynomials in tree age were fitted for the five response variables and the best fit for each, based on the significance of the regression coefficients, was selected. The number of heartwood rings expanded quite rapidly to 0.81 ring per year, at the cost of sapwood ring expansion which averaged 0.19 ring per year.
Effect of promoter sequence on transient expression of the β-glucuronidase gene in embryogenic calli of Larix × eurolepis and Picea mariana following microprojection

The transient expression of the β-glucuronidase reporter gene was compared in embryogenic cell lines of Larix × eurolepis (L. decidua × L. leptolepis) and Picea mariana after introduction of eight vectors containing different promoter sequences using the Dupont Biolistic™ particle delivery system. Transient β-glucuronidase gene expression was highest in cells of both species after bombardment using the wheat abscisic acid inducible Em gene promoter. Transient β-glucuronidase gene expression was comparable in P. mariana and L. × eurolepis for all vectors, with the exception of the rice actin promoter that yielded higher activity in P. mariana than in L. × eurolepis. The Em gene promoter proved inducible by abscisic acid; upon the addition of abscisic acid to the culture medium, β-glucuronidase gene expression was increased 2.3- and 4.4-fold for L. × eurolepis and P. mariana, respectively. Investigation of β-glucuronidase gene expression over time showed that all transient activity disappeared 16 days after.
Persistência de agrotóxicos utilizados na cultura do milho ao parasitoide "Trichogramma pretiosum" Riley, 1879 ("Hymenoptera Trichogrammatidae")

The high yields in corn have been achieved due to various technical factors, being the pest control one of the most important. In this way, the objective was to evaluate the persistence of the pesticides used in corn field to the parasitoid Trichogramma pretiosum. It was evaluated the persistence of seven insecticides and three fungicides, which were separately diluted to 200L of water and sprayed on the vine leaves. These leaves were taken to the laboratory and used into cages at 3, 10, 17, 24 and 31 days, where remained confined the adults of the parasitoids to contamination. The adult mortality of T. pretiosum was measured according to the lower number of parasitized eggs of alternative host Anagasta kuehniella. The results were compared with the witness treatment and pesticides classified according to IOBC categorization. Four replicates for each treatment were used. The fungicides Opera, Priori Xtra and Folicur 200 EC were short life (class 1). The insecticides Match EC and Sumithion 500 CE were short life (class 1); Lorsban 480 BR and Safety were moderately persistent (class 3), and Engeo Pleno, Karate Zeon 50 CS and Tracer were persistent (class 4) to adults of T. pretiosum.
A rye bran diet, rich in plant lignans, has no influence on the composition of the gut microflora in postmenopausal women

The consumption of phytoestrogens has been related to a reduced risk of hormone-dependent cancer types as well as coronary heart diseases. Plant lignans that represent one class of phytoestrogens are found in relatively high concentrations in rye bran. When consumed, they are metabolized into mammalian lignans (enterodiol and enterolactone) by gut bacteria. In order to investigate whether an increased intake of plant lignans had an impact on the composition of the predominant bacterial community of the human gut a 2×6-week intervention study, with a crossover design, was conducted. Eighteen healthy postmenopausal women (age 55–71 years) were recruited and randomly assigned to two groups. The intervention comprised bread products with either rye bran or an inert wheat cellulose (Vitacel®). Faecal samples were collected before and at the end of each intervention period and analysed for their predominant bacterial species composition by a cultivation-independent approach – polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The rye bran diet had no impact on the composition of gut microflora. However, the DGGE profiles demonstrated unique bacterial communities for each individual, which implied a differing efficiency among individuals to metabolize lignans.