Miracle-dz/UniFAR-FTUs huggingface dataset:
Role and Regulation of Autophagy During Developmental Cell Death in Drosophila Melanogaster : A Dissertation

Autophagy is a conserved catabolic process that traffics cellular components to the lysosome for degradation. Autophagy is required for cell survival during nutrient restriction, but it has also been implicated in programmed cell death. It is associated with several diseases, including cancer. Cancer is a disease characterized by aberrant cell growth and proliferation. To support this growth, the tumor cell often deregulates several metabolic processes, including autophagy. Interestingly, autophagy plays paradoxical roles in tumorigenesis. It has been shown to be both tumor suppressive through cell death mechanisms and tumor promoting through its cytoprotective properties. However, the mechanisms regulating the balance between cell death and cell survival, as well as the metabolic consequences of disrupting this balance, are still poorly understood. Autophagy functions in both cell survival and cell death during the development of Drosophila melanogaster, making it an ideal model for studying autophagy in vivo. My research aimed to better understand the regulation and metabolic contribution of autophagy during cell death in Drosophila. I found that the Ral GTPase pathway, important to oncogenesis, regulates autophagy specifically during cell death in Drosophila larval salivary glands. Contrary to previous studies in mammalian cell culture, Ral is dispensable for autophagy induced during nutrient deprivation suggesting that Ral regulates autophagy in a context-dependent manner. This is the first in vivo evidence of Ral regulating autophagy. I found that disrupting autophagy has an extensive impact on an organism’s metabolism. Additionally, I found that autophagy in degrading tissues is crucial for maintaining the fly’s metabolic homeostasis, and that it may be important for resource allocation amongst tissues. This research highlights the importance of understanding how pathways regulate autophagy in different cell contexts and the metabolic outcomes of manipulating those pathways. This is especially important as we investigate which pathways to target therapeutically in an effort to harness autophagy to promote cell death rather than cell survival.
Immune responses to dietary inclusion of prebiotic-based mannan-oligosaccharide and β-glucan in broiler chicks challenged with Salmonella enteritidis

This study was performed to evaluate the effect of dietary prebiotic-based mannan-oligosaccharide and b -glucan on immune organ weights, white blood cell profiles, and antibody titers against Newcastle and infectious bursal disease viruses in broiler chicks challenged with Salmonella enteritidis. The addition of prebiotics to the diet of unchallenged chicks had no effect on antibody titers and other measured parameters. Salmonella challenging decreased the relative weights of immune organs, increased white blood cells and the heterophil-to-lymphocyte ratio, and decreased the antibody titers against Newcastle and infectious bursal disease viruses. Inclusion of prebiotics to the diet of challenged chicks increased the relative weight of the spleen, decreased the heterophil-to-lymphocyte ratio, and increased antibody titers. The results showed that dietary inclusion of prebiotic-based mannan-oligosaccharide and b -glucan has no significant effect on immune parameters on chicks in the noninfected group, but it displays an efficacy on chicks in the group infected with pathogens and can improve the immune responses and health of infected chicks.
Physicochemical Properties of Eight Popular Glutinous Rice Varieties in Korea

Abstract The physicochemical properties of eight popular glutinous rice varieties (Hwasunchal, Dongjinchal, Sangjuchal, Seolhyangchal, Jinbuchal, Sangnamchal, Hangangchal, Milyang-167) in Korea were evaluated. The starch granules in Seolyangchal, Sangnamchal, Hangangchal, and Milyang-167 rice showed greater crystallization than that of the other varieties, which were more loosely packed with larger air spaces in between granules. Dongjinchal rice showed lowest amounts of potassium and calcium with 44.51 and 3029.50 ppm, respectively. This variety also exhibited the highest sugar content with 1.30–16.82 μg g-1 and fastest hydrolysis rate of 771.5 mg g-1. Sangnamchal, Sangjuchal, and Jinbuchal varieties showed abundant amounts of essential amino acids and highest pasting values (73.6°C, 3.0 min). On the other hand, lowest pasting values (69.6°C, 2.7 min) and total amino acid content of 452.61 ng mg-1 were observed in Milyang-167 rice. Hwasunchal and Sangnamchal samples contained the highest concentration of unsaturated fatty acids with 760 mg g-1 and lowest level of saturated fatty acids with 230 mg g-1. The highest viscosity values were obtained in Hangangchal variety, while the lowest values were found in Jinbuchal sample. This study illustrates the wide variation in the physicochemical properties of the glutinous rice varieties analyzed. The results could serve as baseline information for the quality evaluation of rice with unique characteristics suitable for specialty food processing.
Is there a refuge for ants in litter accumulated at the base of Attalea attaleoides (Barb.Rodr.) Wess.Boer (Arecaceae)

The influence of the litter accumulated in the base of the acaulescent palm Attalea attaleoides (Barb. Rodr.) Wess. Boer on the composition of litter-dwelling ants in an upland rainforest in Central Amazon was investigated. The ant fauna was sampled from the litter of the base of 80 palms and in the open litter away from the palms. A list of 76 species identified and other 45 morphotypes is presented and their abundance is compared between microhabitats (litter trapped in the base of the palms and open litter). Our results suggests that the litter trapped in the palm base may be a refuge for non-dominant species, as the presence of aggressive ants in these microhabitats was relative rare. The litter trapped in the palm bases was occupied mostly by unaggressive predator and fungus-grower species, which probably find more prey or better conditions to cultivate their food there.
Body size does not predict species richness among the metazoan phyla

We present a comparative study of the relationship between body size and described taxonomic diversity in the Metazoa. We find no pattern between body size and taxonomic diversity; neither the smallest organisms nor organisms at an intermediate body size are consistently more diverse than their closest relatives. This conclusion holds for both nonphylogenetic analysis, in which phyla are treated as independent points, and analysis of independent contrasts using several recent hypotheses of metazoan phylogeny. These results appear surprising in the context of existing models of body size distributions. However, such models are built around the prevalence of right‐skewed distributions and we find no evidence for such a distribution.
Frost hardiness and cold-storage tolerance of the root system of Picea sitchensis, Pseudotsuga menziesii, Larix kaempferi and Pinus sylvestris bare-root seedlings.

During the winter of 1990–91, fine roots of 2‐year‐old, undercut and wrenched Pseudotsuga menziesii, Larix kaempferi, Pinus sylvestris, and Picea sitchensis (Alaskan, Queen Charlotte Islands, and Oregon) were tested using electrolyte leakage for frost hardiness and tolerance to storage at +1°C for 30 and 90 days as excised roots. Pseudotsuga menziesii and P. sylvestris showed only minor changes in root frost hardiness with a maximum of — 4°C and — 7°C respectively. Larix kaempferi and P. sitchensis developed much greater root frost hardiness; L. kaempferi had a maximum hardiness of — 12°C while P. sitchensis (Queen Charlotte Islands) reached — 13°C during the winter. The root frost hardiness of P. sitchensis increased with the provenance's latitude. There were clear species and provenance differences in the level of long‐term cold‐storage tolerance attained, increasing in the order P. menziesii, P. sylvestris and P. sitchensis (Oregon), L. kaempferi, P. sitchensis (Queen Charlotte Islands), and P. sitchen.
Effect of Open Field and Open Shade Conditions on the Growth and Phytochemical Constituents of Amaranthus cruentus

The growth and phytochemical constituents of Amaranthus cruentus plants under open shade and open field conditions were studied . Plants grown under open field had significantly higher plant height, number of leaves, fresh weight, dry weight and leaf area throughout the period of the analysis than those grown under open shade. Plants grown under open field condition had significantly higher (p = 0.05) amount of total flavonoids and total tannin and total antioxidant capacity. Nevertheless, the total phenol was significantly higher in plants grown under open shade condition. Leaf extracts of plants grown under open field condition also had significantly higher DPPH scavenging activity based on the IC 50 value (38.31 ? g/ml) than those of plants grown under open shade (52.35 ? g/ml). The results of this study show that Amaranthus cruentus plants should be grown under open field to obtain better vegetative growth as well as higher phytochemical and antioxidant capabilities. KEY WORDS : Amaranthus cruentus , open field, open shade, growth, antioxidant
General discussion: Suckling stimulus and lactation

Lactation in the rat can be prolonged indefinitely by the provision of a succession of young foster fitters to continue the stimulus of suckling. Under these conditions lactation becomes a steady state. In three rats nursing their third or fourth litters, lactation was so maintained for periods of 9, 10 and 12 months, respectively, and failure occurred only after the experimental conditions were deliberately altered. To attain steady lactation, foster litters were nursed only for the last few days of the period during which they depend wholly on the mother, i.e. shortly before their eyes open, and thus furnish a strong suckling stimulus not varying too greatly at each exchange of foster litter. In these circumstances sufficient milk was being secreted continuously to increase litter weight by 9 to 10 g per day (figure 49). The oestrous cycle was prolonged, the mean cycle length for the three females during prolonged lactation being 17.8 days. This condition has been described by Selye (1934) as ‘suckling pseudo-pregnancy'. In other experiments with prolonged lactation mating was allowed to take place after periods varying from 50 to 106 days of continuous lactation. There was no diminution of milk production as judged by litter growth over the night of mating if the male was introduced into the female’s cage and the young allowed to remain so that suckling continued. Neither was there a delay in implantation such as occurs after a mating at post-partum oestrus in the presence of a suckling litter, parturition occurring after the normal gestation period of 22 to 23 days (five out of five females).
OPTIMIZING MODELS OF DOLPHIN AUDITORY SENSITIVITY USING EVOLUTIONARY COMPUTATION

ABSTRACT Object classifiers that attempt to mimic dolphin echolocation require an auditory weighting function representative of dolphin peripheral auditory processing. An evolutionary program (EvPg) was used to fit the frequency-dependent output of a bank of bandpass filters to the auditory sensitivity of the bottlenose dolphin, Tursiops truncatus. Pseudo-Gaussian (PG) and rounded exponential (ROEX) functions were used to describe individual filter shapes. Variables determining the number of filters per model, overall filter shape and amplitude scaling were submitted to the EvPg for optimization. Maximum deviation (P e ) between model output and the sensitivity of the dolphin was used as a measure of similarity between the two, i.e., lower P e indicated a greater similarity. The number of filters converged upon 37 for all ROEX models and ≤ 45 for all PG models. The P e of the best-performing PG model was 0.08, and for all ROEX models was 0.13. Greatest deviations typically occurred below 5 kHz and above 130 kHz. Relative audiometric sensitivity of a dolphin ear model has been improved relative to previous models, thereby providing an auditory weighting function more representative of dolphin peripheral auditory processing. This model will be applied to further investigate how dolphins use echolocation to discriminate among objects.
Processing cellular spheroids for histological examination

Abstract Cellular spheroids are three-dimensional cell cultures that mimic native tissues and produce their own extracellular matrix. Spheroids are being used in research for basic science, developmental biology, cancer biology, tissue engineering, drug discovery, and toxicity testing. As spheroids become increasingly used in these applications, it is critical to understand and visualize cells and extracellular matrix content over time. Standard histological methods cannot be applied for fixation and processing of spheroids due to their small size and delicate nature. Given this, there is a need to develop a method to prepare and process spheroids for histological sectioning and examination. A technique was developed for preparing spheroids and tissues composed of spheroids for histological examination, using cellular spheroids for tissue engineering applications.
Bacterial-mediated terrestrial carbon in the foodweb of humic lakes

Taipale, Sami Bacterial-mediated terrestrial carbon in the foodweb of humic lakes Jyväskylä: University of Jyväskylä, 2007, 61 p. (Jyväskylä Studies in Biological and Environmental Science ISSN 1456-9701; 183) ISBN978-951-39-3006-6 (PDF), 978-951-39-2963-3 (nid.) Yhteenveto: Bakteerivälitteisen terrestrisen hiilen merkitys humusjärvien ravintoketjussa Diss. The aim of this thesis was to quantity the relative role of allochthonous dissolved organic carbon (DOC) and autochthonous primary production in the food webs of humic lakes during different seasons. Terrestrial detrital organic matter received from the surrounding catchment area is further decomposed by bacteria in lakes, and in stratified lakes much can be decomposed under anoxic conditions, resulting in high production of methane. However, it has been unclear how much of this decomposed carbon is assimilated by bacteria and then transmitted via zooplankton to higher trophic levels. Carbon stable isotope tracer measurements and 13C-manipulations in a small humic lake, Mekkojärvi, combined with different models, were the basic experimental approaches in this study. Phospholipids fatty acids (PLFA) analyses provided additional insights. Laboratory experiments confirmed that low δ13C values of Daphnia originated from consumption of methane-oxidizing bacteria (MOB) and in situ decrease in δ13C of zooplankton was detected during autumn 2004. Results from enclosures indicated that Daphnia in the lake used multiple food sources, while carbon mass balance calculations suggested that MOB could supply all Daphnia carbon demand during autumn. IsoSource modelling of data from the whole-lake manipulation, revealed that Daphnia consumed heterotrophic bacteria (HB), photoautotrophic green sulphur bacteria (GSB), and MOB in addition to phytoplankton, but the relative contribution of these putative food sources varied seasonally. Overall, the study indicated that Daphnia diet in Mekkojärvi comprised 29-59%, 65-79% and 76-86% bacterial-mediated carbon of allochthonous origin during spring, summer and autumn, respectively. Results from four lakes with different DOC content sampled in spring and autumn 2006 indicated that heterotrophic bacteria have a proportionally higher role as terrestrial carbon mediators in the lower DOC content lakes, whereas chemoautotrophic bacteria and MOB have a particularly important role in very dystrophic lakes.
Cellular and humoral immune defenses of Oxya japonica (Orthoptera: Acrididae) to entomopathogenic fungi Metarhizium anisopliae

One Indonesian isolate of the fungus Metarhizium anisopliae, named Majalengka strain, was evaluated not only for its virulence but also for the immune response of rice grasshopper Oxya japonica (Orthoptera: Acrididae) as a target organism. Five aqueous suspensions with different conidia concentrations in logarithmic series were prepared. The fungus showed high virulence as it caused 100% mortality at low conidia concentration (1.5 × 102 conidia/mL). Remarkable changes in the cellular and humoral responses were also observed when adult grasshoppers were infected with the fungus. The number of hemocytes decreased significantly within 12 h after infection. In addition, the total number of granulocytes increased rapidly in the first 12 h then gradually decreased 24 and 48 h after infections, while the number of coagulocytes fluctuated over time. The infection influenced the humoral response by increasing the phenoloxidase activity.
Isolation and characterization of microsatellites in a perennial Apiaceae, Eryngium alpinum L

In order to investigate the genetic structure in an endangered Alpine plant (Eryngium alpinum L.), we developed microsatellites. Two different approaches were used: an enrichment protocol and the classical technique of hybridization on nylon membranes. We identified 25 loci, 13 of which revealed to be polymorphic. The polymorphism was rather low (2–6 alleles; H E = 0.49 ± 0.16), probably due to the short size of microsatellites (6–10 dinucleotide repeats) and to the fine spatial scale investigated. However, these markers are expected to provide a new insight about the genetic processes at work within and among E. alpinum populations.
Mammalian Development: A Practical Approach

Abbreviations, Introduction, Mouse husbandry Isolation, culture and manipulation of pre-implantation mouse embryos Isolation, culture and manipulation of post-implantation mouse embryos Meiotic analysis in germ cells of man and the mouse Karyotyping and sexing of gametes, embryos and fetuses and in situ hybridization to chromosomes Cell marking techniques and their application Biochemical microassays for x-chromosome-linked enzymes HPRT and PGK Qualitative analysis of protein changes in early mouse development Construction of cDNA libraries for pre-implantation mouse embryos In situ hybridization to messenger RNA in tissue sections Production of transgenic mice Nuclear transplantation in fertilized and parthenogenetically activated eggs The low temperature preservation of mouse oocytes and embryos Fertilization of human oocytes and culture of human pre-implantation embryos in vitro Appendix Index
Characteristics of Ruminal Fermentation of Wethers Fed Tofu Cake Silage with Ethanol

Tofu cake added with three levels of ethanol was made into silages and fed to four wethers to investigate characteristics of ruminal fermentation. The animals received a basal diet consisting of the second cut Orchardgrass hay and beet pulp (4:1) and either fresh tofu cake (control) or one of silages made of tofu cake added with ethanol at 2%, 4% and 6% levels was also fed so that it account for 20% of the whole ration. Feeding levels were determined based on metabolic body size and were restricted to 85% of voluntary intake levels. 1) The animals fed with tofu cake silages had different ruminal fermentation compared to those in the control. There were positive or negative linear effects of amount of ethanol added to tofu cake silage on ruminal pH, volatile fatty acid (VFA) and other parameters. 2) The higher the levels of ethanol added to tofu cake silage the higher the total VFA, acetic, valeric and caproic acid levels and adversely the lower the propionic acid levels. 3) The animals fed with tofu cake silages had significantly (P<0.01) higher ratios of propionic acid to acetic acid in the rumen fluid. 4) Rumen fluid taken from the animals fed with tofu cake silages had lower pH and lactic acid than that from the control. 5) Although there were no apparent increase in pH, total VFA level or any particular VFA levels in the rumen for the amount of tofu cake fed to the animals in this study, further investigations for optimum feeding levels of tofu cake are needed.
Quantifying the effects of stream habitat on populations of breeding Pacific salmon

Recognizing the mechanisms by which environmental conditions drive population dynamics can greatly benefit conservation and management. For example, reductions in densities of spawning Pacific salmon (Oncorhynchus spp.) have received considerable attention, but the role of habitat characteristics on population sizes of breeding salmon is not fully understood. We studied relationships between habitat characteristics and stream population densities of spawning chum (Oncorhynchus keta) and pink (Oncorhynchus gorbuscha) salmon in 44 streams in the Great Bear Rainforest of coastal British Columbia, Canada, with individual streams as the unit of comparison. Our results indicate that a small number of habitat characteristics are important in predicting population density of spawning chum and pink salmon in streams, namely pH for chum salmon and riparian slope and large wood volume for pink salmon. This is the largest multivariable comparison to examine habitat-population relationships in adult spawning salmon and may provide useful quantitative emphasis in guiding management.
Effects of Lake Size on Phytoplankton Photosynthesis

Phytoplankton photosynthesis (PP) was measured for 6 yr in seven remote Canadian Shield lakes that stratify fully during the summer and have water renewal times > 5 yr but vary from 29 to 34 700 ha; Lakes Nipigon and Superior were also studied in two years. Chlorophyll and PP at optimum light were low in the smallest and largest lakes and increased systematically to values nearly five times higher in midsized lakes (~103 ha). Daily PP per square metre of lake surface and annual PP per cubic metre of the mixed layer also varied in this manner, but annual PP per square metre was high in large lakes (despite their low density rates) because of their long growing seasons. Additional data are needed to determine whether the photosynthesis maximum in midsized lakes is inherently size related or an accidental statistical result. Intraannually, chlorophyll-based photosynthesis parameters (, αB) were similar in all lake sizes, but interannually they varied by two to three times; this interannual variation was sign.