Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Cleaners and Sanitizers on Listeria monocytogenes Attached to Product Contact Surfaces.

A variety of chemical cleaning and sanitizing compounds were evaluated for their ability to remove and/or inactivate surface adherent Listeria monocytogenes . Adherent cells were obtained by incubating 1-cm2 chips of stainless steel or plastic conveyor belts with a multistrain cocktail of L. monocytogenes for 24 h at 25°C. Resistance of adherent cells to sanitizers was dependent upon the surface studied, being greatest on polyester/polyurethane followed by polyester and stainless steel. Biofilm removal with cleaners followed the same pattern as sanitizers with the polyester/polyurethane surface being most difficult to clean. Complete biofilm removal and/or inactivation was obtained in many cases where the surface was first cleaned prior to exposure to sanitizer. The data support conventional wisdom in that cleaning must precede sanitizing in order to remove and inactivate microorganisms. Listeria biofilms should be controllable by combining Good Manufacturing Practices with the discipline of a Hazard Analysis Critical Control Point Program.
Constraints on first reproduction in North American red squirrels

Age at first reproduction influences lifetime reproductive success of individuals and growth rates of populations, and is thus of general interest to ecologists. In red squirrel (Tamiasciurus hudsonicus) populations, yearlings and older nulliparous females (age two and above) are less likely to have a litter than multiparous females (i.e. those that have bred before). To explain these life history traits we tested several hypotheses for why particular females fail to breed in a given year. In a five-year study of red squirrels in a jack pine (Pinus banksiana) forest in central Alberta, Canada, the probability of primiparity (i.e. producing a litter for the first time) was correlated with cone crop size, but doubling the caches of cones available to females failed to increase the probability of first time reproduction. Cones were never completely depleted on any territory, so first reproduction rarely appeared to be restricted by absolute food availability on a territory. We hypothesize, that first reproduction is constrained by the squirrel's ability to obtain seed energy enclosed in serotinous cones that vary in distribution on a territory. We found that the probability of primiparity is lower and more variable between years than that of multiparity, because foraging and cone-handling efficiencies vary more in younger than in older squirrels. Nulliparous females given sunflower seeds to reduce handling time were two to six times more likely to produce a first litter than controls extracting seed from jack pine cones. Small body size, inexperience with seed extraction from serotinous cones, and a lack of strategies for gathering and using cones from a new territory are supported as mechanisms that constrain primiparity, especially in yearlings. Cold spring temperatures added a further constraint in one year, as did absolute cone crop size. Multiparous females strip the bracts off cones in the autumn, reducing handling costs in winter and spring, while young nulliparous females lacked such behavioural compensation. In jack pine, reproductive success of red squirrels depends upon behaviour adapted to a seed supply that is abundant but costly to extract from serotinous cones.
Identification of common and distinct epigenetic re-programming properties of Core-Binding Factor (CBF) Fusion Proteins

RUNX1, also known as CBFa, is a master regulator of haematopoiesis. In Acute Myeloid Leukaemia (AML) it is frequently disrupted by translocations to different epigenetic regulators, resulting in the expression of core-binding factor fusion proteins. We compared the chromatin landscape of t(8;21) and t(3;21) AML which express RUNX1-ETO and RUNX1-EVI1, respectively. We found that the diverse clinical outcomes of patients with these two forms of AML are reflected in fundamental differences in gene expression and chromatin landscape. Despite both fusion proteins sharing a RUNT DNA binding domain, we show that RUNX1-EVI-1 targets a more immature stem cell-related gene expression program of genes as compared to RUNX1-ETO. Despite the differences in the epigenomic landscape of t(3;21) and t(8;21) leukaemia, knockdown of either core-binding factor fusion protein activates a common myeloid differentiation program involving up regulation of C/EBPa. By blocking C/EBPa DNA binding through a dominant negative partner, we showed that this factor is required for the downstream effects of RUNX1-EVI-1 knockdown. Even in the continued presence of RUNX1-EVI-1, ectopic expression of C/EBPa. is sufficient to initiate myeloid differentiation in t(3;21) cells. Overall, this suggests that deregulation of C/EBPa is a common pathway in the development of both t(8;21) and t(3;21) AML.
Infrared thermometry and the crop water stress index. II : sampling procedures and interpretation

Infrared thermometry can be a valuable research and production tool for detecting and quantifying water stress in plants, as shown by a large volume of published research. Users of infrared thermometers (IRT) should be aware of the many equipment, environmental, and plant factors influencing canopy temperature measured by an IRT. The purpose of this paper is to describe factors influencing measured plant temperature, outline sampling procedures that will produce reliable Crop Water Stress Index (CWSI) values, and offer interpretations of CWSI and plant temperatures relative to crop production and other water stress parameters by reviewing previously conducted research (.)
Dinámica de la comunidad zooplanctónica (excepto protozoa) en la laguna del Parque Norte, Medellín (Antioquia, Colombia)

Con el fin de evaluar la estructura de la comunidad de zooplancton y la variación temporal de su densidad, y además, con el propósito de establecer las variables climáticas, físicas, químicas y biológicas asociadas a ella, se realizaron muestreos semanales de zooplancton y mensuales de las variables ambientales, en una estación de la laguna Parque Norte, Medellín (Antioquia, Colombia) durante el período comprendido entre mayo de 1999 y febrero de 2000. Se encontró que la comunidad zooplanctónica estaba compuesta principalmente por tres especies: el copépodo calanoide Arctodiaptomus dorsalis, el rotífero Brachionus plicatilis, y el branquiópodo cladócero Moina macrophtalma. De estas tres especies, A. dorsalis fue la especie que presentó mayor cantidad de individuos durante casi todo el tiempo de muestreo. Mientras que los valores de dominancia fueron bajos, los de equidad fueron altos, debido a la codominancia que presentaron los morfotipos de A. dorsalis. La variación temporal de la estructura numérica de la comunidad fue poco inconstante, lo cual se explicó por los bajos coeficientes de variación que presentaron los índices de riqueza numérica, equidad y dominancia. La dinámica temporal de los distintos estadios de la comunidad zooplanctónica, resumida en el coeficiente de variación, fue alta. La misma fue mayor para ambas clases de edad de M. macrophtalma, para los copepoditos I a V y para las hembras ovadas de B. plicatilis. Los menores cambios en la dimensión tiempo de muestreo fueron presentados por los machos y hembras no ovadas de A. dorsalis y por las hembras no ovadas de B. plicatilis. Se encontró alta asociación entre los integrantes de la comunidad, debido a que ocupan nichos diferentes lo que atenúa la competencia entre ellos. Las variaciones en la densidad de la comunidad zooplanctónica dependieron del aumento o la disminución de Botryococcus braunii, el alga dominante en la laguna.
Histochemical Studies of Protein Accumulating Process in Rice Grain

Protein is contained in the rice grain in the largest quantity next to starch, and supposed to be concerned with the transparency process of rice grain. In this report, we studied protein distribution in rice grain, protein accumulating process, and protein amount related to nitrogen fertilizer, rice quality which is classified by white portion in grain and varieties. The result are summarized as follows; 1. Protein was observed by ninhydrin reaction, and section was pre-treated with perchloric acid as solvent of starch grain. 2. Protein is distributed in outer layer of endosperm except for aleuron layer, richer on ventral side, and less on dorsal side and in central part of endosperm. 3. We did not notice any protein coloration by ninhydrin solution in pericarp, seed coat and aleuron layer. 4. Protein accumulates from outer layer of endosperm to inner layer, while starch accumulates from center line of grain to outer layer of endosperm. 5. Grains of heavily nitrogen applied plot were richer in protein than normally fertillized plot. 6. White ventral part grain and white core grain were richer in protein than fully ripe grain. The development of grain was rapid. White basal part grain was less in protein. It is because of poor ripening. 7. Early varieties were richer in protein than late varieties except for Koshisakae having germinated seed caused by lodging.
Bromeliales, Related Monocots, and Resolution of Relationships among Bromeliaceae Subfamilies

Cladistics, phenetics, and our understanding of chromosomal evolution were applied to questions of the relationships and resemblances among the three subfamilies of the monocot family Bromeliaceae. This large, distinct family (2100 species) is mostly from the new world tropics. Among 10 possibly closely related families to the monotypic order Bromeliales, Velloziaceae of Bromeliflorae appear to be the most likely to share the same common ancestor with Bromeliacae, though other members of Bromeliflorae (and some Zingiberiflorae and Commeliniflorae) are also implicated by the analyses. Nearly all of these sister taxa have the same effect in polarizing mor- phological and anatomical characters. Cladistic analyses placed Bromelioideae and Tillandsioideae as sister taxa and the third subfamily, Pitcairnioideae in close proximity to the family's putative ancestor. A possible explanation of the revealed, multiple lineage relationships and phenetic re- semblances among families is a hybrid, paleopolyploid origin of Bromeliaceae. Chromosome num- bers are in accord with this notion of reticulate evolution having occurred during the origin of the monotypic order, Bromeliales.
Simulated Drought Affects Male Reproductive Function in Deer Mice (Peromyscus maniculatus bairdii)

Reproduction stops during the breeding season of many rodent populations, including Peromyscus maniculatus. The proposition that water availability mediates the midseason breeding hiatus in male deer mice was evaluated in the present study. Paired testicular and epididymal weights (absolute and relative to body mass) were reduced after 10 wk of restricted water consumption. Spermatogenesis was also impaired by limited water intake. Blood plasma testosterone concentrations were reduced, but plasma luteinizing hormone (LH) titers were unaffected by water restriction. Finally, the number of offspring sired was reduced in mice with restricted access to water. Carcass water content did not significantly differ between animals with restricted (25% of ad lib.) or unrestricted access to water; however, body mass was reduced about 15% after chronic water intake restriction. Although reproductive function (i.e., reproductive organ mass, plasma testosterone titers, and sperm counts) was significantly depressed in water-restricted mice, the reproductive systems of about 25% of the animals were relatively unaffected by water restriction. In order to study the physiological factors associated with individual reproductive responses to water restriction, animals were rank ordered according to their epididymal sperm numbers; individuals in the top (Q₁) and bottom (Q₄) quartiles of epididymal sperm counts were further compared. Water-restricted Q₁ deer mice did not significantly differ on any parameter from mice with ad lib. access to water. No water-restricted Q₄ deer mice possessed any epididymal sperm. Deer mice in Q₄ significantly reduced paired testicular and epididymal masses as compared with animals in the top quartile. It was important that Q₄ deer mice reduced their body mass by 34%. Plasma LH titers were significantly depressed in Q₄ animals as compared with Q₁ mice or mice with ad lib. water. Body fat content was also reduced only in the Q₄ deer mice. Taken together, these findings suggest that water availability may act as an extrinsic cue to suppress fertility in deer mice independently of temperature and day length and somewhat independently from food because despite an absolute reduction in food consumption with the onset of water restriction, food intake corrected for body mass did not differ. Animals that stopped reproductive function (Q₄ mice) lost substantial body fat and total mass. Water-restricted males that maintained body fat levels also maintained reproductive function. Differential hydrolysis of adipose tissue in response to decreased testosterone titers may account for the phenotypic variation in reproductive responsiveness to water restriction. These results are discussed in terms of their ecological and evolutionary implications.
Morphological variation of Thalassia testudinum in two shallow coastal environments from the southeastern Gulf of Mexico

Abstract Total biomass, shoot density, leaf length and leaf width of the dominant seagrass Thalassia testudinum were compared between two coastal environments in the northeastern part of the Yucatan peninsula (Mexico). The coastal environments were (a) an exposed sublittoral zone (<1 km from the shoreline) and (b) a sheltered coastal lagoon. Plant morphology was monitored at monthly intervals from June 2001 to May 2002. There was a clear morphological variation between coastal environments throughout the period of study. In the exposed sublittoral zone, total biomass and shoot density were lower and leaves were longer and wider. In contrast, in the sheltered lagoon, total biomass and shoot density were higher and the leaves shorter and narrower. Overall, high values of total biomass, shoot density and leaf width were observed during the warm weather seasons (rainy and dry) whereas the low values were observed during the cold fronts weather season (nortes); leaf length followed a reverse trend. Results presented here stress the need to take into account the natural pattern of morphological variation in the design of sampling and monitoring programs.
Using plant traits to compare sward structure and composition of grass species across environmental gradients

Abstract Plant traits which may give an indication of a plant's strategy for nutrient acquisition and regeneration are known for numerous grassland species. This study aimed to establish whether there is any relationship between two plant traits: specific leaf area (SLA) and number of reproductive tillers, and sward structural characteristics which influence herbage intake by grazers (bulk density and digestibility, leaf:stem ratio). Comparison is made for nutrient-rich (Dactylis glomerata) and nutrient-poor (Festuca rubra) grass species. We hypothesized that these traits are responsive to environmental gradients and also act on the processes of the ecosystem. Both grasses were compared with two P-fertilizer rates in two localities (200 and 1300 m a.s.l.) which differed in their temperature:radiation ratios. For the vegetative phase SLA was well correlated with sward characteristics: D. glomerata, which has the higher SLA, has the lower bulk density and higher digestibility. The values of SLA and vegetation bulk density varied according to growing conditions (P-rate and temperature:radiation ratio), but the ranking of the species remained the same because the phenotypic plasticity that exists for plant traits was also observed for sward structure and composition. That suggested the possibility of grouping natural grassland species for their relevant characteristics for grazers according to SLA values. Over the reproductive phase, the proportion of stems was well correlated to the percentage of reproductive tillers. However, the percentage of reproductive tillers was a very plastic trait for both species, depending on the growing conditions, and resulting in a density-dependent effect, particularly for F. rubra. The species studied were too plastic and too similar in their regenerative strategy so that there is no unique relationship between percentage of reproductive tillers and stem proportion, regardless of the species and the growing conditions. The number of reproductive tillers is not a suitable plant trait which could be used to rank species for leaf and stem proportions in the sward. Abbreviations: DM = Dry matter; LAR = Leaf area ratio; LWR = Leaf Weight Ratio; SLA = Specific Leaf Area.
Bactericidal Treatment of Hatching Eggs I. Chemical Immersion Treatments and Salmonella

Abstract Breeder flocks and commercial hatcheries represent the earliest and probably the most critical control points for salmonellae entry into commercial integrated poultry operations. Effective chemical treatment of hatching eggs may also be a necessary part of reducing the presence of salmonellae on processed broiler carcasses. This study evaluated the immersion of artificially inoculated eggs into three chemicals: phenol, hydrogen peroxide (H2O2), and polyhexamethylenebiguanide hydrochloride (PHMB) following various inoculum drying times of 1 min, 5 min, 4 hr, and 24 hr. Reductions in Salmonella-positive eggs for the various chemicals as compared to the water-treated controls were as follows: 1) 0.78% phenol: 80% reduction at 1 min, 0% reduction if the egg was treated 24 hr after contamination; 2) 2.0% H2O2: 85% reduction at 1 min, 25% reduction at 24 hr; 3) 0.05% PHMB: 93% reduction at 1 min, 12% reduction at 24 hr. These data demonstrate that chemical treatments do not consistently kill all Salmonella on or in eggshells and that what effectiveness they have appears to diminish as the amount of time between contamination and treatment increases.
Developing a bioinformatics framework for proteogenomics

In the last 15 years, since the human genome was first sequenced, genome sequencing and annotation have continued to improve. However, genome annotation has not kept up with the accelerating rate of genome sequencing and as a result there is now a large backlog of genomic data waiting to be interpreted both quickly and accurately. Through advances in proteomics a new field has emerged to help improve genome annotation, termed proteogenomics, which uses peptide mass spectrometry data, enabling the discovery of novel protein coding genes, as well as the refinement and validation of known and putative protein-coding genes. The annotation of genomes relies heavily on ab initio gene prediction programs and/or mapping of a range of RNA transcripts. Although this method provides insights into the gene content of genomes it is unable to distinguish protein-coding genes from putative non-coding RNA genes. This problem is further confounded by the fact that only 5% of the public protein sequence repository at UniProt/SwissProt has been curated and derived from actual protein evidence. This thesis contends that it is critically important to incorporate proteomics data into genome annotation pipelines to provide experimental protein-coding evidence. Although there have been major improvements in proteogenomics over the last decade there are still numerous challenges to overcome. These key challenges include the loss of sensitivity when using inflated search spaces of putative sequences, how best to interpret novel identifications and how best to control for false discoveries. This thesis addresses the existing gap between the use of genomic and proteomic sources for accurate genome annotation by applying a proteogenomics approach with a customised methodology. This new approach was applied within four case studies: a prokaryote bacterium; a monocotyledonous wheat plant; a dicotyledonous grape plant; and human. The key contributions of this thesis are: a new methodology for proteogenomics analysis; 145 suggested gene refinements in Bradyrhizobium diazoefficiens (nitrogen-fixing bacteria); 55 new gene predictions (57 protein isoforms) in Vitis vinifera (grape); 49 new gene predictions (52 protein isoforms) in Homo sapiens (human); and 67 new gene predictions (70 protein isoforms) in Triticum aestivum (bread wheat). Lastly, a number of possible improvements for the studies conducted in this thesis and proteogenomics as a whole have been identified and discussed.
IMPACT OF PRE- AND POST–HARVEST APPLICATIONS OF NATURAL ANTIMICROBIAL PRODUCTS ON APPLE AND PEAR SOFT ROT DISEASE

Three natural antibacterial compounds including bacteriocin like substance (BLS) produced from lactic acid bacteria (LAB), ethanolic extract of propolis (EEP), and nine plant extracts were evaluated against soft rot Bacillus strains. Testing in vivo these compounds were evaluated to control pear and apple soft rot disease. Among eight BLS tested, BLS of LAB2, LAB105 and LAB 107 exhibited the highest antibacterial activity as indicated by the formation of clear inhibition zone. Propolis extracts exhibited significant antibacterial activity against all tested soft rot Bacillu s strains and it was noticed that the antibacterial activity was concentration dependent. Among nine plant extracts tested, extracts of Eucalyptus globulus and Psidium guajava exhibited the highest antibacterial activity. All tested antibacterial products significantly decreased apple and pear soft rot severity caused by Bacillus altitudinis compared to untreated control. The highest reduction percentage of soft rot severity was recorded for EEP followed by BLS from LAB and plant extracts tested, respectively. Combined pre-and post-harvest treatments of apple and pear with antimicrobial compounds proved to be more effective in reducing the soft rot severity and improved the physical and chemical properties of fruits during storage in both years of the study. The natural antimicrobial agents used in this study were promising compounds, since it seems to be more safe, economical and great potential for extending the shelf life and improve the quality of fruits. Therefore, the application of these compounds in the control of apple and pear soft rot could be advantageous for consumers, producers, and the environment.
15-Deoxy-Δ12,14-prostaglandin J2 induces apoptosis of a thyroid papillary cancer cell line (CG3 cells) through increasing intracellular iron and oxidative stress

Treatment of carcinoma cell lines with 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2), a natural ligand of the peroxisome proliferator-activated receptor-&ggr;, has been reported to induce apoptosis and/or inhibit proliferation. In this study, we investigated the cytotoxic effect and the action mechanisms of 15d-PGJ2 in a thyroid papillary cancer cell line, CG3. The results indicate that 15d-PGJ2 caused cytotoxicity and increased the amount of intracellular reactive oxygen species (ROS) in these cells. Mitochondrial oxidative phosphorylation inhibitors (carbonyl cyanide m-chloro-phenylhydrazone, oligomycin, cyclosporin A and rotenone), NADPH oxidase inhibitor (diphenyleneiodonium), xanthine oxidase inhibitor (allopurinol) and NO synthase inhibitor (N-monomethyl-l-arginine acetate) did not reduce the generation of ROS. However, catalase, N-acetyl-cysteine and the iron chelator desferri-oxamine decreased the intracellular ROS of 15d-PGJ2-treated CG3 cells. Furthermore, 15d-PGJ2 enhanced the accumulation of iron in the CG3 cells. These data suggest that 15d-PGJ2 induces the generation of ROS by enhancing the accumulation of intracellular iron and that the increased oxidative stress may cause apoptosis of CG3 cells.