Miracle-dz/UniFAR-FTUs huggingface dataset:
Survival of encapsulated probiotic bacteria during storage at low water activity at ambient temperature

Probiotics are defined by FAO/WHO (2001) as microorganisms that improve the healthiness of the host when available in sufficient number in the human intestinal tract. Health benefits of probiotic bacteria are correlated with the number of viable bacteria reaching the host and the recommended bacterial population required is ≥107 CFU/g. Besides during processing and storage, probiotic bacteria are required to survive during transit in gastrointestinal tract with very low pH (1.8 – 2.0), in bile juice and pancreatin before beneficial effects are realized in the lower small intestine and colon. Microencapsulation is effective in ensuring bacterial viability which is influenced by the type of encapsulating materials, the methods used for encapsulation and storage thereafter for a given bacterium. The use of microencapsulating materials is to entrap or immobilize probiotic bacteria within microcapsule and to protect the bacteria during the drying process, which is the last stage of microencapsulation. The objectives of this thesis were to study the effect of different types of microencapsulants (alginate or casein-based formulations), and drying methods (freeze and spray drying) on survival of probiotic bacteria for 10 weeks of storage at 25oC (ambient temperature) at low water activities (aw). Three probiotic bacteria (Bifidobacterium animalis ssp. lactis Bb12, Bifidobacterium longum and Lactobacillus acidophilus) and one strain of most sensitive lactic acid bacteria (L. lactis ssp. cremoris) to acid and bile environment were encapsulated and selected functional properties, such as survival, acid and bile tolerance, surface hydrophobicity, and retaining of some of the enzyme activities were investigated. The protective mechanism of microencapsulation was studied by determinations of microstructures using Environment Scanning Electron Microscopy (ESEM), interactions with cellular components by Fourier Transform Infrared Spectroscopy (FTIR), and glass transition temperature (Tg) measurements by Differential Scanning Calorimetry (DSC).
Characteristics of pH, Total Acid, Total Soluble Solid on Tomato Juice by Ohmic Heating Technology

Tomatoes ( Solanum lycopersicum L.) are important vegetables all over the world and are consumed in both fresh and processed form. Tomatoes as food can be processed into tomato juice by using Ohmic heating technology. The ohmic heating technology in food processing is essentially a process in which liquid food, solids, or mixtures between the mare simultaneously heated by passing an electric current through it. Foods passed by an electric current give a response in the form of heat generation internally on foodstuffs due to the electrical resistance. This study aims to determine changes in pH, total acid, total soluble solids in tomato juice which heated at 70°C, 90°C and 110°C and duration time of heating; 15minutes, 30minutes and 45 minutes. The results showed that the temperature and duration of ohmic heating significantly affect the change of pH value and total tomato juice. The total acid value decreases as well as the lower the pH by the longer the heating. While total soluble solids are increasing by the higher temperature and heating time.
CHARACTERIZATION OF THE ECOLOGICAL AND PHYSIOLOGICAL BASIS OF SUPERIOR RHIZOSPHERE COLONIZATION BY 2,4-DIACETYLPHLOROGLUCINOL-PRODUCING FLUORESCENT PSEUDOMONAS GENOTYPES

by Leonardo De La Fuente, Ph.D. Washington State University December 2005 Chair: David M. Weller Rhizosphere isolates of Pseudomonas fluorescens producing the antibiotic 2,4diacetylphloroglucinol (2,4-DAPG) are effective biocontrol agents, and are responsible for the suppressiveness of some soils to soilborne pathogens. The diversity within a worldwide collection of 2,4-DAPG-producers was assessed by sequencing phlD, a key gene in the 2,4-DAPG biosynthetic locus. Phylogenetic analyses resulted in groupings similar to those previously identified by BOX-PCR (genotypes A-Q and T). Exploiting polymorphisms in the sequence of phlD, allele-specific PCR primers were designed for the detection of strains of six genotypes. The primers allowed quantification of populations of strains competing in the rhizosphere. Soil was inoculated with all possible
Preliminary characterization of a Tritrichomonas foetus-like protozoan isolated from preputial smegma of virgin bulls

Trichomonad isolates from 14 virgin beef bulls in 3 California herds were submitted to the California Veterinary Diagnostic Laboratory for confirmation of a diagnosis of bovine trichomoniasis. Specimens were submitted in self-contained diagnostic pouches and produced cultures with a protozoan like Tritrichomonas foetus. Under bright-field microscopy, large numbers of single-celled motile organisms, approximately 12 μm x 9 μm, with multiple anterior flagellae, a posterior flagellum, axostyle, and a clearly visible undulating membrane were detected. Motility was jerky and rolling. Air-dried smears of cultures stained with Giemsa or Diff-Quick/iodine revealed an organism similar to T. foetus, although somewhat more rounded (less spindle-shaped). Several organisms appeared to have 4 flagellae, and there were numerous dark-staining bodies in the cytoplasm. Scanning electron micrographs (5000 X) clearly showed four anterior flagellae and an undulating membrane on most organisms, and an axostyle that was consistently longer than that seen in T. foetus. Specific primers for T. foetus were used in a polymerase chain reaction (PCR) assay. No amplification product was detected from any of the "virgin bull" isolates, while positive control isolates of T. foetus all yielded an amplicon of the expected size. On the basis of this partial morphological and molecular characterization, it was tentatively concluded that the isolated organism is not T. foetus, and speculate that it may be a commensal organism of the lower bowel. The recovery of non T. foetus trichomonads in a commercially available diagnostic system suggests that more specific methods may be needed for discrimination among trichomonads isolated from the preputial cavity of bulls.
Yield and nutrient uptake of transplanted rice (Oryza sativa) with different moisture regimes and integrated nutrient supply

A field experiment was conducted during kharif 2010 at Faizabad (Uttar Pradesh) to assessthe effects of moisture regime and integrated nutrient supply on yield, yield attributes and nutrients uptake of transplanted rice (Oryza sativa L.). Irrigation with 7 cm water at 1 day after disappearance of ponded water (DADPW) was superior to 3 and 5 DADPW in respect of yield, yield attributes and nutrient uptake. The highest grain yield (5.44 t ha−1) and straw yield (7.68 t ha−1), was recorded with 1 DADPW. Application of recommended dose of NPK (120:60:40 kg ha−1) applied through inorganic fertilizers was at par with green manuring + 75% NPK through inorganic fertilizers in respect of yield attributes, yield and total nutrient uptake. The maximum grain yield (5.21 t ha−1) and straw yield (7.45 t ha−1) was obtained with 100% NPK (120:60:40 kg ha−1), which was at par with green manuring + 75% NPK applied through inorganic fertilizers.
Tropane alkaloids elicitation of black henbane parts with calcium and nitrogen application under hydroponics culture.

Black henbane (Hyoscyamus niger L.) an species in Solanaceae family has long been used as a medicinal plant, which is well known for their alkaloid secondary metabolites mainly hyoscyamine and scopolamine. Industrial synthesis of these compounds is difficult due to their complex chemical structure so the compounds are extracted from Solanaceae family plants. This study examined the effects of various calcium (Ca) and nitrogen (N) concentrations (0, 16.6, 33.3 and 50 mg.L -1 as Ca0-Ca3 and N0N3) on henbane roots and leaves dry weight and their two main alkaloids content under hydroponics culture. Results showed the highest hyoscyamine content (4.6 g/g.10 -2 and 2.69 g/g.10 -2 ) were obtained at N2Ca2 in total foliage and root dry weight, respectively. Also, the highest scopolamine content (14.51 g/g.10-2 and 7.77 g/g.10-2) were obtained at N1Ca2 and N2Ca2 in total foliage and root dry weight, respectively. In henbane plants, hyoscyamine content of leaves were increased significantly with increasing nitrogen and calcium concentration up to N3Ca3 treatment, while the largest leaf scopolamine content was observed in the N3Ca1 treatment. In the roots, biosynthesis location of alkaloids, maximum hyoscyamine and scopolamine content were observed under N3Ca2 and N3Ca3 treatments, respectively. Results also showed that hyoscyamine and scopolamine content of roots under N3Ca2 and N3Ca3 conditions were almost 67% and 64% higher than that of control plants, respectively. The largest plant total alkaloids accumulation was observed in fertilized plants under N3Ca1 treatment, which showed the highest elicitation index (65.70). It seems that calcium and nitrogen fertilizer are essential nutrient elements necessary for henbane growth and metabolism, which could be considered as abiotic elicitor or precursor in alkaloid biosynthesis pathway.
Hereditary and induced modifications of the normal necrotic patterns in the developing limb buds of the rat and mouse: facts and hypotheses

Similar patterns of physiological cell death appearing according to a precise and predictable schedule can be observed in the developing limb buds of mouse and rat embryos in relation to well defined regional features of limb morphogenesis. They characterize either the apical ectodermal ridge or delineated areas of the undifferentiated mesoderm. Four kinds of modified necrotic patterns have been demonstrated in relation to the genesis of different limb malformations: the absence of cell death in particular areas which are normally affected, excessive cell death occurring on schedule in normal sites, advanced, prolonged or delayed cell necrosis in normal sites, and abnormal cell degeneration unrelated to the normal necrotic pattern. With the exception of the latter category which is more specifically related to chemically induced limb malformations, the first three categories characterize both hereditary and provoked teratological situations.
Spider (Araneae) species activity, crop type and management factors in an extensive plot trial.

Spider species activity in five crop types, with organic and conventional fertility and crop protection management, was assessed using pitfall traps in 2005. Significant differences in activity between crop types were seen with 16 species, with 14 most active in grass/clover and 12 least active in vegetable plots. Within crops there were 20 significant responses to fertility, with 16 more active in conventional plots. Crop protection management produced four significant models, with three preferences for organic management. Small linyphiid species showed a distinct preference for the densest vegetation on conventionally fertilised plots, whilst the larger lycosid species were more active on the more open organic plots. In general, there was more activity in conventionally managed crops, in contrast to other reports.
Distribution and Alkaline phosphatatase activity of filamentous conjugales in an upper Teesdale stream

Two small streams in Upper Teesdale National Nature Reserve were examined with respect to water chemistry and filamentous Conjugales present. Phosphate, nitrate and ammonia concentrations in the water were determined, to investigate a possible link between the nutrient status water and phosphatase enzyme activity of the algae. It has been shown that phosphatase activity is inducible in some algae under conditions of low inorganic phosphorus availability. Phosphatase enzymes enable the algae to hydrolyse organic phosphorus, converting it into a more easily utilised form. A connection was found at Red Sike between nutrient, especially organic phosphorus, levels and phosphatase activity. Algae were also sampled from subjectively determined microhabitats in Red Sike and Slapestone Sike, to investigate if particular community assemblages were more common in certain microhabitat sites.
The Oil Price Volatility and a Revisited Saudi Import Demand Function: An Empirical Analysis

The focus of this paper is to analyze theoretically and empirically the effects of a non-linear oil price shocks on Saudi import demand function covering the period of 1970–2015, utilizing unrestricted vector autoregressive (VAR) approach. Johansen’s testing procedure result asserts the existence of stable long-run relationship between real aggregate import demand (RIM), oil price shocks (OILPI and OILPD), real gross domestic product (GDP), relative price (RP) and last year real foreign exchange (RFEt-1). The findings confirm that the oil price shocks affect negatively RIM. The signs are not as expected and significant. Moreover, the coefficients had little magnitude and effects. Nonetheless, the income elasticity is greater than one, had the right sign, and statistically significant. The price elasticity is negative as expected and significant. As predicted in literature, foreign exchange coefficient is negative, but is not statistically significant. Although the oil price shocks are significant, their magnitudes are weak. This could be attributed to the strong effects that come from traditional import demand determinants.
The Putative Cannabinoid Receptor GPR55 Modulates Synaptic Plasticity in the Hippocampus

The Putative Cannabinoid Receptor GPR55 Modulates Synaptic Plasticity in the Hippocampus Corinne Marie Badgley Department of Physiology and Developmental Biology, BYU Master of Science in Neuroscience Endocannabinoids (eCBs) are small molecules that are capable of modulating synaptic plasticity of both excitatory and inhibitory synapses in the brain. While eCBs bind to transient receptor potential vanilloid 1 (TRPV1) and cannabinoid receptor 1 (CB1) in the central nervous system, we recently identified a form of non-CB1, non-TRPV1 mediated long term depression activated by the eCB anandamide at CA1 hippocampal stratum radiatum interneurons. GPR55, an orphan G-protein receptor, has been identified in the hippocampus and is capable of activation by eCBs, making it a good candidate for mediating this non-CB1, non-TRPV1 form of synaptic plasticity. Here we performed whole-cell patch clamp recordings from CA1 stratum radiatum interneurons in rat brain slices to investigate the effect of GPR55 agonist O-1602 on excitatory synapses. We also performed field recordings from CA1 pyramidal cells in rats and GPR55 knockout mice and littermate controls to investigate the effect of GPR55 agonists O-1602 and lysophosphatidylinositol (LPI) on both basal output and electrically induced long-term depression and long-term potentiation in the hippocampus. Application of O-1602 in rats depressed long-term potentiation in CA1 pyramidal cells, and depressed excitatory glutamatergic transmission onto some interneurons. O-1602 had no effect on long-term depression of CA1 pyramidal cells. GPR55 +/+ mice showed an increase in long-term potentiation in the presence of LPI compared to GPR55 littermates. GPR55 mice had no change in long-term potentiation when exposed to O-1602, though there was an increase in post-tetanic potentiation with O-1602. In order to examine whether GPR55 has a role in formation of spatial memory, GPR55 -/mice were compared to littermate controls during a Morris water maze behavioral task, with a reversal task after 7 days of training. GPR55 mice did not perform in a different manner on either the training task or the reversal, though there may be a trend of difference in training worth investigating further. This study illustrates a novel pathway for synaptic plasticity modulation through GPR55 in the hippocampus, and may therefore provide valuable insight into both the effects of synthetic and endogenous cannabinoids on the brain and the processes underlying learning and memory.
Molecular mechanisms in muscular dystrophy : a gene expression profiling study.

The muscular dystrophies are a group of neuromuscular disorders characterized by progres¬sive muscle weakness and wasting. Although the underlying genetic defects of a large number of muscular dystrophies are now know, the molecular mechanisms resulting in the devastating effects of the disease are not yet clear. Furthermore, the muscular dystrophies differ in clinical presentation and severity. The processes responsible for this di¬vergence are largely unknown as well. In this thesis, gene expression profiling has been applied to study the molecular and cellular mechanisms and subsequent biological processes that play a role in muscular dystrophy. To characterize the processes associated with regeneration, we have compared gene expression levels in hindlimb muscle tissue of mdx and control mice in a temporal study. Additionally, we have determined the gene expression profiles of dif¬ferentiating human myoblasts in vitro, since regeneration processes recapitulate myogenesis. We also set out to compare gene expression levels of different mouse models for muscular dystrophy to find common and distinct molecular mechanisms that underlie different forms of muscular dystrophy. Accordingly, we first had to determine the effects of genetic background variation between inbred mouse strains, and to study the feasibility of alternative experimental designs.
Telomere and Proximal Sequence Analysis Using High-Throughput Sequencing Reads

The telomere is a specialized simple sequence repeat found at the end of all linear chromosomes. It acts as a substrate for telomere binding factors that in coordination with other interacting elements form what is known as the shelterin complex to protect the end of the chromosome from the DNA damage repair machinery. The telomere shortens with each cell division, and once critically short is no longer able to perform this role. Short dysfunctional telomeres result in cellular senescence, apoptosis, or genome instability. Telomere length is regulated by many factors including cis-acting elements in the proximal sequence which is known as the subtelomere. The Riethman lab played a pivotal role in generating the reference sequence of the subtelomere in both the human and mouse genomes, providing an essential resource for this work. Short high throughput sequencing (HTS) reads generated from the simple repeat containing telomere or the segmental duplication rich subtelomere cannot be aligned to a reference genome uniquely. They are filtered and excluded from many HTS analysis methods. A ChIP-Seq analysis pipeline was developed to incorporate these multimapping reads to study DNA-protein interactions in the subtelomere. This pipeline was employed to search for factors regulating the expression TERRA, an essential long non-coding RNA, and to better characterize their transcription start sites. ChIP-seq analysis in the human subtelomere found colocalization of CTCF and Cohesin directly adjacent to the telomere and throughout the subtelomere specific repeats. Follow up functional studies showed this binding regulated TERRA transcription at these sites. Extending these analyses in the mouse genome showed very different patterns of CTCF and cohesin binding, with no evidence of binding at apparent sites of TERRA transcription. Mouse subtelomere sequence analysis showed the cooccurence of two repeats at sites of putative TERRA expression, MurSatRep1 and MMSAT4, one of which was previously shown to be expressed in lincRNAs. The Telomere Analysis from SEquencing Reads(TASER) pipeline was developed to capture telomere information from HTS data sets and used to investigate telomere changes that occur in prostate cancer. TASER analysis of 53 paired prostate tumor and normal samples revealed an overall decrease in telomere length in tumor samples relative to matched paired normal tissue, especially sequence containing the exact canonical telomere repeat. Multimapping reads contain important information, that when used properly, help elucidate understanding of telomere biology, cancer biology, and genome regulation and stability. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Genomics & Computational Biology First Advisor Harold Riethman This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1460
Effect of different concentrations of metals ions on Bacillus and Pseudomonas spp. isolated from industrial effluents of Faisalabad.

*Corresponding Author Robina Ali robina_ali@ymail.com With the intention to determine effects of different metals on growth of bacteria that were previously identified as heavy metal resistant, total six bacterial samples were selected, repurified and reidentified from the bacterial isolates. Different morphological and biochemical tests were performed that differentiated bacteria into two genera i.e. Bacillus sp. and Pseudomonas sp. Bacteria was grown at pH 7 and temp of 37oC up to incubation time of 96 hours. Three metals (Na, Ca, Zn) were used with concentrations ranged between 25-200 mg/ml. It was found that as the concentrations of metals increased, growth of Bacillus and Pseudomonas spp. firstly increased and then decreased in case of all selected metals. Lowest growth occurred at 200 mg/ml of metal concentration. Optical density at 600 nm was considered as a measure of growth of bacteria. As growth increased, optical density increased and vice versa. Na was found to have a more negative effect on growth of bacterial isolates as compared to other two metals that is, Ca, Zn. Bacillus sp. under investigation was found to be more resistant to these metals as compared to Pseudomonas sp. Both bacterial isolates showed their maximum growth after 72 hours of incubation in most of the cases, afterwards growth decreased. Decreasing resistance pattern for both of bacterial species was as follows; Ca > Zn > Na. The findings revealed the potential application of Bacillus and Pseudomonas spp. for the removal of heavy metals from industrial wastewaters under the conditions where salts of Sodium, Zinc and Calcium are present.
SEROPREVALENCE AND ISOLATION OF CHICKEN INFECTED WITH SALMONELLA HAEMATOLOGICAL AND PATHOGICAL EVALUATION

The research was conducted to study seroprevalence of bird infected with salmonella and to evaluate the pathology of the affected cockerel chicken in Abia and Umudike both in Aba north and Ikwuano local government area of Abia State, as well as isolate salmonella. This study was carried out from February to June, 2010. Samples used were blood cloaca and liver swabs. Other organs like intestine, ovary, spleen and lungs were also used. The serum plate agglutination method was used. Others are gross, histopathology, morphological, cultural and biochemical tests. The total percentage of seroprevalence was 45.0%. Gross lesion showed congestion, enlargement of the liver and petechial hemorrhages in the intestine. Hematological features showed that there were decreased red blood cells on hemoglobin while the white blood cells increased. And there was no significance difference. (P<0.05). At history, congestion, massive lymphocytes infiltrates in the liver paranchyma. The sum of 54 seropositive salmonella samples from birds were isolated. Further study would also be carried out to investigate the pathogenesis, serotyping and sensitivity test.