Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic regulation of embryonic and intestinal stem cells by DNA hydroxymethylation

DNA methylation at the 5 position of cytosine is a well-characterized epigenetic modification that is important for essential cellular processes including stem cell proliferation and differentiation. 5-methylcytosine (5mC) can be oxidized by the Ten Eleven Translocation (TET) family of enzymes to 5-hydroxymethylcytosine (5hmC), which has been suggested as either an intermediate in DNA demethylation or as an independent epigenetic modification that directly regulates gene expression. Gene silencing and activation are important processes in embryonic stem cells (ESCs) and intestinal stem cells (ISCs) for their self-renewal and differentiation, but our understanding of the potential role of 5hmC and TET hydroxylases in these processes is still limited. Here, I generate genome-wide maps of the 5hmC mark in ISCs and their differentiated progeny and utilize Tet1-/mice model to investigate the role of TET1 in the intestinal epithelium. Genes with high levels of hydroxymethylation in ISCs are strongly enriched for developmental regulation functions. The Tet1-deficient postnatal intestine shows significantly reduced numbers of proliferative cells and decreased Wnt target genes expression, which correlates with lower 5hmC levels at their promoters. These data demonstrate that Tet1-mediated DNA hydroxymethylation is important for the self-renewal of the intestinal epithelium. To determine a novel role of 5hmC, we perform integrative analyses of various epigenomic sequencing datasets, and identify a group of distal transcription factor binding sites as putative silenced enhancers, which are lacking active histone marks and nascent transcription, but are nevertheless highly enriched for the 5hmC modification in ESCs. During lineage specification of ESCs, these silenced elements lose 5hmC and acquire the H3K4me1/2 histone marks and become active. I demonstrate that these elements function as enhancers when the 5hmC mark is removed by a reporter assays. These data suggest that 5hmC suppresses the activity of a specific subset of enhancers in ESCs. In summary, DNA hydroxymethylation contributes to both transcriptional activation and repression for epigenetic gene regulation in stem cells. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Klaus H. Kaestner This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1814
Repair and genetic consequences of DNA double strand breaks during animal development

The genetic code of life is stored in DNA molecules that consist of two parallel strands of coupled nucleotides that form a DNA double helix. One of the most deleterious forms of DNA damage is a DNA double-strand break (DSB) in which both strands of the helix are broken. When not repaired adequately DSBs can lead to extensive loss of genetic information and/or genomic rearrangements, ultimately fueling genome instability, cellular dysfunction and malignant transformation. This thesis describes several studies conducted to examine how living organisms preserve their genetic material and how different DNA repair pathways influence genome stability. To study these questions the nematode C. elegans was used as a model organism, as it allows efficient genetic manipulation as well as in-depth genetic analysis of mutagenic processes. We exploited these unique attributes to i) convert these animals into in vivo sensors of DNA damage ii) identify factors not implicated in genome stability before, iii) unveil mechanisms that dictate DNA repair pathway choice, and iv) determine the biological consequences of endogenous barriers that impede DNA replication.
Milk Production and Body Weight Change of Cross-Bred Dairy Cows as Affected by Walking Distance and Breed Variations

The study was conducted in Bako Agricultural Research Centre, in Western Ethiopia with objectives of assessing the impact of breed and walking distance on milk production. Two breeds of dairy cows (50% Horro X 50% Friesian= HF and 50% Horro X 50% Jersey= HJ) were used to conduct this experiment. The cows were assigned to three walking distance groups: WD0= grazing around the barn, WD1.5= grazing 1.5km away from the barn and WD3.0= grazing 3km away from the barn. The experiment was arranged as a 2 x 3 factorial in RCBD. A total of 36 cows uniform in previous lactation milk yield and at mid stage of lactation were involved in the study, and they were grouped into two based on the period of joining the experiment. The result showed that the mean daily milk yield of cows was higher (p<0.05) for WD0 cows than WD3.0, while milk yield of WD1.5 cows was not different from WD0 or WD3.0. The mean protein content of milk from HF cows (27.03 g/kg) was significantly higher (p<0.05) than HJ cows (25.2 g/kg). The mean milk protein content of cows in WD1.5 (27.8 g/kg) was significantly (p<0.05) higher than those inWD0 and WD3.0. The mean milk fat composition of HJ cows (57.7 g/kg) was significantly (p<0.05) higher than HF cows (51.0 g/kg). HF cows lost weight while HJ gained during the experimental period. Dairy cows in WD0 had higher mean body weight and better gain compared to those walked 1.5 and 3.0 km. This study further demonstrated that the loss of BW at longer distance of 3.0 km was higher for HF (-4.1 kg) compared to HJ (-1.0 kg) cows. Keywords: Horro cows; walking distance; milk yield; cross-bred dairy cows
Great Expectations: Correlations between Pollinator Assemblages and Floral Characters in Lamiaceae

Premise of research. Pollination syndromes are used to infer pollinators from floral attributes when field observations of floral visitors are lacking. Such inferences are often found to be incorrect or too generalized. To investigate the relationship between pollinators and observable differences in a genus of Lamiaceae with flowers that appear ornithophilous and entomophilous, we experimentally quantified floral morphology and pollinator assemblages in a phylogenetic perspective. Methodology. Floral morphology was examined using multivariate analysis of geometric morphometrics (corolla shape described by landmarks), linear dimensions, and nonmetric attributes for 17 species of Prostanthera. Pollination effectiveness was determined through censuses of floral visitors and interactions by pollinators with flowers, and multivariate statistics were used to examine correspondence between these data and nonlandmark characters. Ancestral state reconstruction was performed using geometric morphometric data and a phylogenetic tree. Pivotal results. Three floral morphologies were identified in Prostanthera, each of which was associated with a unique pollinator assemblage and corroborated by our detailed field observations. A higher abundance of bees visited flowers with the ancestral (bee) floral type, which had a long corolla, porrect adaxial lobes, and long anther appendages. Visits by birds were more frequent to the derived bird floral type, characterized by red or green flowers with larger nectar volumes, longer and narrower corollas, and a reflexed abaxial lobe. Another derived lineage attracted a higher abundance of generalist flies and beetles (beetle+fly floral type). This lineage had flowers with a shorter corolla tube, reflexed adaxial lobes, and shorter anther appendages. Conclusions. When pollinator frequency was used as a proxy for pollinator effectiveness, the correspondence between the floral types and pollinator assemblages supported traditional concepts of bird and insect pollination syndromes. Intermediates between these floral types also corresponded with phylogenetic position and pollinator assemblage. Linear measurements of floral attributes were just as reliable as landmark data in predicting pollinator assemblages. By combining a molecular phylogeny with the above data, evidence indicated that the bird and beetle+fly floral types diversified from an ancestral bee floral type, demonstrating at least one evolutionary specialization for birds, as well as another shift toward a more generalized pollination syndrome. This combination of techniques presents a potential application with which to investigate the evolution of pollination.
Economic values for lean meat and fat efficiency in Norwegian Landrace nucleus pig population

ABSTRACT A profit function was developed to estimate economic values for new efficiency traits for fattening pigs in Norwegian Landrace. These traits were lean meat efficiency (LME) and fat efficiency (FE). LME and FE described how much feed the animal used to produce 1 kg lean meat and fat as a deviation from the mean. Both traits were derived from analysing total feed consumption in a random regression model which included lean meat and fat content of the carcass (FC) as random covariates. In addition, economic values and breeding values were calculated for days from 40 to 100/120 kg live weight (DAYS), lean meat percentage (LMP) and FC. To compare LME and FE with total feed intake (FI), two indexes were constructed. One index included LME, FE, DAYS, LMP and FC and was referred to as breeding goal A and one index included FI, LMP and DAYS and was referred to as breeding goal B. The standardized economic values for LME and FE were 8.9 and 2.9 EUR/σa, respectively. There was a larger variation in the index for breeding goal A (SD = 5.65) than B (SD = 3.97). The results suggested that the two efficiency traits had an economic importance in pork production and that there was a potential for increased genetic gain in profit by using breeding goal A compared to breeding goal B.
Digestive System of the Cephalocarid Hutchinsoniella Macracantha

The digestive tract of the cephalocarid Hutchinsoniella macracantha begins with an atrium oris, posterior to the mouth. The esophagus loops up through the head and ends with a valve to the midgut. The epithelial cells and cuticle of both these structures are connected with long, winding, apically distended microvilli. The midgut is a straight tube with a pair of diverticula anteriorly. Midgut epithelial cells have microvilli, light vesicles, and a peculiar endoplasmic reticulum that is produced into a palisade of extensions toward the apical surface. Outside the basal lamina are muscle and peri-intestinal cells which send fingerlike projections into the basal portion of the midgut epithelial cells. The rectum joins the midgut near the end of the eighteenth segment and consists of unspecialized epithelial cells. In spite of the simple gross morphology the digestive tract has a complicated musculature. Circular muscles follow the whole tract including the diverticula. Radial muscles attach to the esophagus and rectum. Many longitudinal muscles are found inside the circular muscles in the anterior part of the midgut but only a few outside posteriorly. Gland cells occur in the labrum and diverticula. Absorption of nutrients seems to be limited to the midgut epithelial cells. Metabolites are transported via their endoplasmic reticulum to that of the peri-intestinal cells. (Less)
Outline for Autecological Studies of Range Grasses.

In 1966, range ecologists from the states of Arizona, Nevada, New Mexico, Utah, Washington, and Wyoming2 initiated co-operative Western Regional Project W-90, entitled “Ecological Life Histories of Selected Western Range Plants. ” This group was formed because of recognition that the lack of autecological knowledge on many important western range species was impeding range management progress. Our knowledge of range plants lags considerably behind the foresters’ autecological understanding of the trees they manage. Ready availability of current information to the practicing forester is now possible because of the recent publication of U.S.D.A. Agricultural Handbook 271, Silvics of Forest Trees of the United States. Here the essential information on the autecolo<gy of 125 principal tree species has been assembled through the efforts of about as many authors. The only thing comparable that range men have access to is the Range Plant Handbook, now 30 years out of date and yet recently reprinted. I estimate that only about a dozen native range species have received study comparable to that of the commercially important trees or improved pasture plants. Summarization of all available autecological knowledge under one cover can be found for only about four species. Two of these
Effect of genotype, environment and their interaction on seed and opium yield in opium poppy (Papaver Somniferum L.) and comparison of different stability models for Gei

The present investigation was conducted to identify promising and stable genotypes from 21 advanced breeding lines using Eberhart and Russell model and to compare the suitability and authenticity of the Eberhart and Russell model with various other stability models like Shukla's s(i)(2), Wricke’s W(i)(2)and Tai's λ(i). The analysis of variance for stability revealed highly significant differences between genotypes which suggested that the genotypes differed considerably with respect to yield performance. The linear genotype × environment interaction as well as pooled deviation mean squares were also significant, indicating the presence of both predictable and non-predictable components. Five genotypes LT31, BR231, BR233, BR242 and BR234 were identified as ideal and stable through Eberhart and Russell model and were also confirmed by other stability models. It was concluded that Eberhart and Russell model can be reliably used for the identification of stable opium poppy genotypes over environments.
Growth promotion of maize (Zea mays L.) seedlings by bacterial auxin, in vitro.

Recent research repots have shown that toxic materials from chemical fertilizers can be harmful to humans, animals and the environment. Plant Growth Promoting Bacteria could be a way to reduce chemical fertilizer doses. For this reason we tested the effect of bacterial auxin in relation to maize seeds. Six hybrids of different FAO groups were treated with three concentrations of auxin. Results from this study show that the applied auxin had significant positive effect in relation to improving the maize seeds shoot and root length. The auxin seed treatment which resulted in the positive stimulative effect on shoot and root length had no significant effect on seed germination percentage in comparison to the untreated control seeds.
Functional consequences of realistic extinction scenarios in Amazonian soil food webs

Global biodiversity loss is creating a more urgent need to understand the role organisms play in ecosystem functioning and mechanisms of control. Decomposition of dead organic matter is a key ecological process that ensures soil formation, nutrient availability, and carbon sequestration. To gain understanding of how biodiversity and ecosystems function together to control leaf-litter decomposition processes in a tropical rain forest (Yasuni National Park, Ecuador), we predicted the consequences of the decomposition process using a protocol in which we systematically disassemble the structural functionality of the soil macrofauna communities. We (1) describe the structure and function of the edaphic communities in detail and (2) explore the functional consequences of structural changes in these communities using a non-random exclusion experiment to simulate body size-related extinctions. To do this, we manipulated access of five size classes of soil invertebrates to eight types of plant leaf-litter resources. After measuring and identifying about 4400 soil individuals belonging to 541 morphospecies, 12 functional groups, and following the fate of about 2000 tree leaves in a 50-ha plot, we showed that (1) soil invertebrate communities were composed of a few common and many rare morphospecies that included mostly leaf-litter transformer groups, with the most morphospecies and the greatest abundance coming from Hymenoptera, Collembola, and Coleoptera; (2) our survey captured 63–74% of the total soil biodiversity of the study area (meaning there may be up to 860 morphospecies); (3) litter transformers covered the widest range of body volume, and all groups were evenly distributed at small and large spatial scales (i.e., we found no patterns of spatial aggregation); (4) changes in food web structure significantly altered biomass loss for only three of the eight leaf-litter treatments, suggesting the decomposition process was highly resistant to drastic changes such as size-biased biodiversity loss independent of resource quality. We conclude organic matter decomposition may depend on all non-additive effects that arise from multi-species interactions, including facilitation, interspecific interference competition, and top-down control that predators exert over detritivores at all body size ranges.
Selenium and iron in the rat intestine: effects on lipid peroxidation

Selenium and Iron in the Rat Intestine: Effects on Lipid Peroxidation by Sileny Vega, Doctor of Philosophy Utah State University, 1989 Major Professor: Dr. A. Mahoney Department: Toxicology viii Effects of Fe and Se status on GSHPx activity and lipid peroxidation in liver and intestinal mucosa were studied. Rats were Se and Fe supplemented ( +Se+Fe), Sedeficient and Fe-supplemented (-Se+Fe), Se supplemented and Fe overloaded (+Se++Fe) by intramuscular injection, or Se deficient and Fe overloaded (-Se++Fe) for 20d. Fe overloaded tissues had more Fe, but hemoglobin was unaffected. Liver and mucosal GSHPx activity was low in Se-deficient rats. Thiobarbituric acid reactive substances (TBARS) were higher in Fe overloaded and -Se++Fe vs +Se++Fe tissues. Mucosal TBARS was higher in -Se++Fe rats gavaged with CBrCl3. In experiment 2, Fe overload was induced by a 2% carbonyl iron, low-Se diet fed for 2mo, the +Se++Fe and -Se++Fe groups. Low Se-, low Fe-diet was fed to rats supplemented with Fe or Fe and Se in the water, the -Se+Fe and +Se+Fe controls. Iron overloaded tissues had more Fe. Liver and mucosal GSHPx activity was lower in Se-deficient and +Se++Fe vs +Se+Fe rats. TBARS was higher in Fe overloaded, -Se++Fe vs +Se++Fe, and CBrCl3 tissues. Hemoglobin and serum Fe were lower in the -Se++Fe group. In experiment 3, low-Se, low-Fe diet was fed for 20d, the -Se-Fe, +Se-Fe, -Se+Fe and +Se+Fe groups. Mucosal Fe w s 1 wer i the Fe-deficient rats. Cytochrome P-450 and GSHPx activities were
Insecticidal activity of Cleistanthus collinus Roxb

Fresh leaf juice, decoction and alcoholic extract of Cleistanthus collinus in different concentrations were studied for their insecticidal activity. Leaf decoction (50%) was found to be most effective, where single application was able to kill all the insects within 12 hr and control the insects till harvesting especially rice caseworm (Nymphula depunctalis) a common paddy pest of chhattisgarh region of India. Fresh leaf juice and alcoholic extract at 50% also prevented insect attack on rice crop but with some extent to adverse effect. This present study was carried out on the utilization of plants of local habitat for the benefit of tribal societies.
A taxonomic conspectus of Phrymaceae: A narrowed circumscription for Mimulus, new and resurrected genera, and new names and combinations

A revised taxonomic classification of Phrymaceae down to species level is presented, based on molecular-phylogenetic and morpho-taxonomic studies, setting a f ramework for ongoing work. In the concept adopted, the family includes 188 species divided into 13 genera. All species as currently understood are listed and assigned to genera and sections whic h in several cases have new circumscriptions requiring many new combinations. Four ma in clades are recognized. Clade A . An Asian-African-Australasian-centered clade of 7 genera: Mimulus L. sensu stricto (7 species) of North America, Asia to Africa, and Australasia is sister t o an Australian-centered group that comprises Elacholoma (2 species), Glossostigma (5 species), Microcarpaea (2 species), Peplidium (4 species), Uvedalia (2 species) and a new monotypic genus Thyridia, described here. The remaining three clades are largely American, with a few east Asian spe cies. Clade B. Monotypic Phryma forms its own clade. Clade C . Hemichaena (5 species), Mimetanthe (1 species), and Diplacus (46 species). Clade D. Leucocarpus (1 species) and Erythranthe (111 species). A new infrageneric classification is constructed for the two largest genera –– Diplacus with six sections, and Erythranthe with 12. The sessile to subsessile flowers and parietal placentation of Diplacus distinguish it from Erythranthe, which has long-pedicellate flowers and axile placentation. Descriptions are provided for all inframilial, generic, and infrageneric taxa and full synonymies enable a comparison with previous classifications.
Medicinal Uses of Marijuana and Cannabinoids

ABSTRACT In the past two decades, there has been increasing interest in the therapeutic potential of cannabis and single cannabinoids, mainly cannabidiol (CBD) and delta-9-tetrahydrocannabinol (THC). THC and cannabis products rich in THC exert their effects mainly through the activation of cannabinoid receptors (CB1 and CB2). Since 1975, 140 controlled clinical trials using different cannabinoids or whole-plant preparations for the treatment of a large number of disorders and symptoms have been conducted. Results have led to the approval of cannabis-based medicines [dronabinol, nabilone, and the cannabis extract nabiximols (Sativex®, THC:CBD = 1:1)] as well as cannabis flowers in several countries. Controlled clinical studies provide substantial evidence for the use of cannabinoid receptor agonists in cancer chemotherapy induced nausea and vomiting, appetite loss and cachexia in cancer and HIV patients, neuropathic and chronic pain, and in spasticity in multiple sclerosis. In addition, there is also some evidence suggesting a therapeutic potential of cannabis-based medicines in other indications including Tourette syndrome, spinal cord injury, Crohn's disease, irritable bowel syndrome, and glaucoma. In several other indications, small uncontrolled and single-case studies reporting beneficial effects are available, for example in posttraumatic stress disorder, attention deficit hyperactivity disorder, and migraine. The most common side effects of THC and cannabis-based medicines rich in THC are sedation and dizziness (in more than 10% of patients), psychological effects, and dry mouth. Tolerance to these side effects nearly always develops within a short time. Withdrawal symptoms are hardly ever a problem in the therapeutic setting. In recent years there is an increasing interest in the medical use of CBD, which exerts no intoxicating side effects and is usually well-tolerated. Preliminary data suggest promising effects in the treatment of anxiety disorders, schizophrenia, dystonia, and some forms of epilepsy. This review gives an overview on clinical studies which have been published over the past 40 years.
Antioxidant activity of silkworm powder treated with protease

The antioxidant activity of silkworm powder treated by proteolytic enzyme was investigated. Total protein content of silkworm power was assayed using BCA, Bradford assays and SDS-polyacrylamide gel electrophoresis (PAGE) with alkaline protease treatment conditions including temperature and pH. The optimum condition of alkaline protease treatment for silkworm powder was found to be 60℃ and pH 7. The alkaline protease treatment resulted in increased contents of free amino acids, total polyphenol and total flavonoid compared to control group. The silkworm hydrolysates showed excellent antioxidant activities in various in vitro models such as 2,2 diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, 2,2 - azino-bis(3-ethylbenzthiazoline-6)-sulfonic acid (ABTS) radical scavenging activity. These results provide useful information for using silkworm powder as an ingredient in functional foods and for exploiting alkaline protease treatment to improve the extractability and bioactivity of a raw material.