Miracle-dz/UniFAR-FTUs huggingface dataset:
Next Generation ABO Genetics and Genomics

Next-generation ABO genetics and genomics Patrick Keolu Ozer Fox Chair of the Supervisory Committee: Dr. Debbie Nickerson Department of Genome Sciences Accurately cross matching units of blood based on blood type is essential for successful transfusion therapy. ABO is the most clinically relevant blood group in transfusion therapy due to the presence of naturally occurring ABO antibodies. Failure to correctly match ABO blood type can cause fatal transfusion reactions even in transfusion naïve individuals. The ABO gene commonly encodes two different forms of a glycosyltransferase which adds A or B sugars (N-acetylgalactosamine for A or α-D-galactose for B) to the H-antigen substrate. Single nucleotide variants (SNVs) and insertion-deletions (indels) in the ABO gene affect function at the molecular level by altering the specificity and efficiency of the enzyme for specific sugars (leading to the A1, A2, and B blood types) or by knocking out gene function to generate the O blood type. Thus, variation in A, B, or O serological phenotype is the result of genetic variation in the coding portion of the ABO gene. Currently, approaches to genotype ABO are limited because ABO is a complex locus with a large number of functional haplotypes that can lead to the A, B, or O phenotype. In addition to many other factors, ABO blood type plays a role in determining an individual’s risk for multiple common complex diseases including the number one and number two causes of death in the United States: cardiovascular disease and cancer. However, the influence of specific ABO types and ABO subtype variants, such as the A1 and A2 haplotype/subtypes, on common complex disease risk has not yet been fully explored. In this dissertation, I directly explore the many forms of variation in the ABO gene in diverse human populations using multiple next-generation human genome sequencing datasets, while simultaneously addressing the limitations of both traditional serological methods and existing genotyping methods designed to determine ABO blood type from variation found in the ABO gene. I then discuss strategies and limitations of developing an automated approach to call high resolution phased ABO blood types from NGS data. The methods and analyses outlined in this dissertation can be used to generate higher resolution blood type and subtype calls leveraging the variation and phenotypes within large scale NGS populations based to explore the relationships between rare and common ABO variants, ABO haplotypes, and subtypes with common complex diseaserelated phenotypes (i.e., cardiovascular disease, cancer, and type 2 diabetes). My hope is that the NGS tools developed in this thesis will be used to create a more comprehensive understanding of common complex disease etiology in the future.
Pyrosequencing reveals benthic bacteria changes responsing to heavy deposition of Microcystis scum in lab — searching bacteria for bloom control

Bacteria capable of degrading cyanobacteria Microcystis are crucial for determining the ecological consequences of Microcystis blooms in freshwater lakes. Scum derived from Microcystis blooms tends to accumulate in bays of large lakes and then sink to the sediments where it is finally consumed by benthic bacteria. Understanding the response of benthic bacterial communities to massive Microcystis deposition events may help identify the bacteria best suited to Microcystis hydrolyzation and even bloom control. For that purpose, an experimental system was set up in which intact sediment cores were incubated in the laboratory with normal and heavy deposits of Microcystis detritus. Pyrosequencing was performed in order to describe a phylogenetic inventory of bacterial communities in samples taken at 0–1, 1–2 and 2–3 cm depths in incubated sediments and in original untreated sediment. A hierarchical cluster tree was constructed expose differences between sediments. Similarity percentage calculations were also performed to identify the bacterial species contributing to variation. The results of this study suggest that: (1) deposition of Microcystis scums exerts a strong effect on the bacterial community composition in the surface (0–1 cm) and sub-surface (1–2 cm) sediment layers; (2) bacterial community responses to Microcystis detritus deposition vary across vertical gradients. A list of bacteria with potential roles in Microcystis degradation was compiled. These findings may inform the development of future measures for Microcystis bloom control in lakes.
The Theory of Keratinization

This study was carried out on eight of Awassi ewes in estrus during which keratinization can occur in the animal farm of college of veterinary medicine, Baghdad university in June 2006. In order to study the process of keratinization histologically, samples of vaginal smears were taken and stained by methylene blue. The present study recognized five stages of keratinization namely (stage of mitosis, stage of cellular transformation, stage of cellular adhesion, stage of endogenous bacterial invasion and stage of sloughing), during which the cells undergo a series of transformations in shape, size, colour and cornification. The study found also that the cells were transformed from small spherical basophilic shape to large polygonal acidophilic shape as the polygonal shape was suitable in hidden the interstitial spaces between the cells, when these cells try to building a compact sheet or packet which act as a defensive barrier to protect the internal environment against the external environment, finally the endogenous bacteria metabolize the glycogen into lactic acid which decrease the pH of the vagina and protect it from the pathogenic bacteria. Then these attacked cells start to exfoliated so that, we can regard the process of keratinization as a defensive mechanism in the vagina.
The tonoplast proton-translocating ATPase from the crassulacean acid metabolism plant Kalanchoë daigremontiana

A rapid procedure was developed for the purification and reconstitution into proteoliposomes of the tonoplast H+-translocating ATPase from the Crassulacean acid metabolism (CAM) plant Kalanchoe daigremontiana. It involved the fractionation of crude tonoplast membranes with the detergent Triton X-114, resolubilization of the ATPase with octyl glucoside in the presence of an optimized lipid mixture and formation of liposomes on removal of detergent by gel filtration. The enzyme could be further purified by sedimentation through glycerol gradients. It contained polypeptides of apparent molecular mass 72, 57, 48, 42, 39, 33 and 16 kDa; the smallest of these was labelled by [14C]-dicyclohexylcarbodiimide. There was no evidence for the presence of any large subunits. In these proteoliposomes, ATP hydrolysis and H+-translocation were measured independently, by a coupled enzyme assay and by quenching of the fluorescence of a permeant weak base, respectively. The kinetic properties of the reconstituted plant ATPase were studied in detail. Rate equations derived from theoretical models of the enzyme's behaviour were fitted to experimental data by weighted non-linear regression, using a computer program that calculated the kinetic parameters that accorded to the optimal fit. The dependence of the rate of H+translocation on the concentration of MgATP was well fitted by the Michaelis equation, with a Km value about 30 jaM. ATP could be replaced by dATP, ITP, GTP, UTP or CTP and Mg2+ by Mn2+ or Ca2+; kinetic parameters for these substrates were determined. In contrast hydrolysis of MgATP showed complex kinetics which suggested either negative cooperativity between nucleotide-binding sites, or the presence of two non-interacting catalytic sites. Both the hydrolytic and the H+-translocating activities of the proteoliposomes were inhibited by nitrate, though not in parallel, the latter activity being more sensitive. Both activities were inhibited in parallel by bafilomycin A-,, which did not produce complete inhibition; the bafilomycininsensitive component had complex ATPase kinetics similar to those of the uninhibited enzyme. ADP behaved as an allosteric inhibitor of the ATPase, inducing apparent cooperativity in saturation with MgATP, together with a reduction in Vmax. By fitting the experimental data to the concerted allosteric model proposed by Monod et al. (1965) a theoretical model was proposed in which the complex kinetics were due to the interaction between two substrate binding sites and a single inhibitor-binding site. Antibodies raised against specific subunits of the tonoplast ATPase were shown to cross-react with V-type ATPases from different species. Immunoblotting of the plant antibodies against the V-type ATPase purified from several bovine tissues has suggested the existence of isoforms of this particular enzyme.
Incubation Behaviour of Blue Cyanistes caeruleus and Great Tits Parus major in a Mediterranean Habitat

Abstract. The incubation stage in avian reproduction could be as costly as the nestling rearing stage. This is particularly true in the case of uniparental incubation, during which both current and future breeding attempts may be compromised. Therefore, the knowledge of the proximate effects that condition the incubation behaviour in free-living bird populations is of great importance in understanding the evolution of avian life history. In this two-year study, we assessed the incubation behaviours of Blue Cyanistes caeruleus and Great Tits Parus major inhabiting the same Mediterranean area in central Spain through the usage of iButton data loggers. It showed that the incubating behaviour of our tit populations resembles that reported in previous studies, but with peculiarities related to living at lower latitudes, i.e. with a relatively low attentiveness and a shorter active day. Both tit species showed very different incubation strategies, with Blue Tits leaving more frequently the nest (Mean ± SE number of off-bouts, Blue Tit = 27.14 ± 0.63, Great Tit = 16.95 ± 0.58) but for shorter periods than Great Tits (off-bout duration, Blue Tit = 8.76 ± 0.22 min, Great Tit = 14.04 ± 0.56 min; on-bout duration, Blue Tit = 22.63 ± 0.60 min, Great Tit = 36.86 ± 0.86 min). Nonetheless, both species provided a similar nest attentiveness, percentage of time of the active day during which the females were actively incubating (Blue Tit = 70.87 ± 0.57%, Great Tit = 70.75 ± 0.83%). Presumably, differences in the cooling rate of clutches, estimated with the iButtons, could be behind the differences in incubation behaviour between species and the greater capacity of Great Tits to adjust their incubation behaviour.
The impact of some inorganic substances on change in body mass of Tenebrio molitor (Coleoptera, Tenebrionidae) larvae in a laboratory experiment

Abstract Addition of low concentrations of metal ions to the diet of saprophagous insects can impact on their metabolism over a short period of time, causing an increase or decrease in their body mass. This article presents a 14-day laboratory experiment evaluating the changes in the body mass of larval stage 3 of Tenebrio molitor (Linnaeus, 1758) induced by adding different inorganic substances (350 mg kg−1 of dry fodder) to the diet of the larvae. Following the addition of inorganic substances to the fodder, the most marked differences compared to the control were observed in the groups which consumed substrate with lead nitrate (the mass of the larvae increased on average by 102.6% compared to increase in mass in the control variant of the experiments), cobalt nitrate (by 96.9%), calcium chloride (by 89.1%) sodium triphosphate (by 86.0%), zinc chloride (by 83.5%). A nonsignificant effect (a tendency of increase in the body mass) on T. molitor larvae was caused by manganese sulfate (by 57.8%), aluminium nitrate (by 57.3%), iron oxide (by 51.5%), barium nitrate (by 47.9%), orthophosphoric acid (by 47.4%), manganese chloride (by 46.5%), calcium carbonate (by 27.7%), iron sulfate (by 24.2%) and ammonium heptamolybdate (by –7.5%). Therefore, 5 out of the 15 studied inorganic substances significantly stimulated the increase in the body weight of T. molitor larvae, and 7 manifested these capacities at the level of tendency (stimulated an increase in body weight averaging 43–58% over the 14-day experiment). The obtained data indicate a necessity for further study on the impact of inorganic pollutants on different stages of insects.
Dynamics and structure formation in active actin networks

The actin cytoskeleton of eucaryotic cells undergoes constant remodeling. To shed light on the principles governing such dynamic reorganizations, a reconstituted active actin network is introduced. The structure formation in this minimal model system is the result of an intricate interplay of force exertion by motor filaments and the degree of connectivity in the network: a superdiffusive behavior, which is reminiscent of the intracellular dynamics in living cells, occurs only if these parameters are balanced.
Improving Salt Stress Tolerance of Pineapple cv. Queen Using Cobalt In vitro

This investigation aimed to focus on how cobalt can avoid the damage caused by salinity stress (NaCl) on Pineapple cv. Queen in vitro. Multiplicated pineapple explants (10 – 12 mm) were subjected for eight weeks to different NaCl conc. (0, 65, 135 or 200 mM) half of them were treated firstly with 5 mg/L Cobalt sulphate. Vegetative growth parameters (no.of shoots, no. of leaves, and shoot length/explant), mineral composition (N, P, K, Na, Cl, Fe, Mn, Zn, Cu and cobalt), proline and protein content were determined. Molecular characterization using PCR based RAPD was carried out to describe the genetic differences resulted from the studied treatments, (salinity and salinity combined with cobalt sulfate). Results show that, pineapple explants growth under salt stress wasn ’ t prohibited completely specially below 135 mM of NaCl, but it affected negatively with the highest salt stress 200 mM of NaCl. Explants treated with cobalt before subjected to salinity scored the highest significant percentage of vegetative growth characteristics compared with those untreated. Explants treated firstly with cobalt resulted in a significantly decrease of Na + and Cl - . Cobalt has a positive effect on Macro and Micronutrients, proline and protein content. A total of 34 DNA fragments varying from 186-1456 (bp) were amplified, of which 16 were polymorphic and seven observed as a unique markers that revealed 64.03% polymorphism.
A review of Hamilton Harbour beaches: Towards delisting 2020, successes and challenges

Bayfront and Pier 4 Beaches are located in Hamilton Harbour, Ontario, Canada. Both beaches experienced health advisory postings >60% of the bathing season prior to 2005. In order to de-list Hamilton Harbour as one of 43 areas of concerns, the water quality at Bayfront and Pier 4 Beaches must meet the provincial water quality objective of 100 cfu of Escherichia coli 100 ml−1 > = 80% of the bathing season for a minimum of three consecutive years. In 2005, the Hamilton Harbour Beach Committee was formed to guide beach managers on decisions pertaining to beach remediation and E. coli mitigation. Here we discuss the various studies, projects and public outreach programs delivered by Environment Canada, the City of Hamilton and the Bay Area Restoration Council to improve beach health and move toward delisting as an Area of Concern by 2020.
Cysteine responsive copper(II) based ¹⁹F MRI probes

Cysteine plays an important role upholding cellular homeostasis by maintaining a proper redox environment. Perturbations in cysteine concentration may lead to cardiovascular and liver disease, and cancer, making cysteine an important amino acid to detect and monitor. In order to detect cysteine in vitro and in vivo it is advantageous to choose an imaging tool with high tissue penetration, low background noise, and less radiation, which led us to 19 F MRI. Herein we report a series of copper complexes with fluorine moieties appended to the macrocycle cyclam for use of 19 F MRI detection of cysteine. In this study, an efficient “turn-on” response was observed upon reduction of the Cu(II) complexes by cysteine. This response was characterized using UV/Vis absorption spectroscopy, NMR, EPR, and 19 F MRI. Early biological results suggest that these probes can detect cysteine in red blood cells, opening the doors for further animal studies.
Supplementing lactation diets with herbal extract mixture during summer improves the performance of sows and nursing piglets

Abstract A total of 45 Landrace × Yorkshire multiparous sows were used to evaluate the effect of dietary herbal extract mixture (Scutellaria baicalensis and Lonicera japonica, HEM) supplementation in lactating sows under heat stress. Sows were randomly allotted to 1 of 3 dietary treatments: 1) CON, basal diet; 2) TRT 1, basal diet with 5 g/d HEM; 3) TRT 2, basal diet with 10 g/d HEM. During lactation, dietary HEM supplementation linearly increased (P<0.05) the average daily feed intake (ADFI) and linearly decreased (P<0.05) backfat loss. The digestibility of dry matter (DM) was increased after farrowing (linear, P<0.05; quadratic, P<0.05) and weaning (linear, P<0.05) by HEM supplementation. Furthermore, HEM treatment led to a lower (linear, P<0.01) serum cortisol level. In addition, administration of HEM improved (linear, P<0.05) the piglets weaning weight and overall average daily gain (ADG) during suckling period. Meanwhile, on day 7 and 14 after birth, the fecal score of piglets was decreased (linear, P<0.01) by HEM supplementation. Taken together, under high ambient temperatures, inclusion of HEM to lactation diets could improve the feed intake, digestibility of DM, piglets weaning weight and ADG, while decreasing backfat loss, serum cortisol level, as well as the diarrhea of piglets.
Food Composition for Blue Mussels (Mytilus edulis) in the Menai Strait, UK, Based on Physical and Biochemical Analyses

ABSTRACT To clarify the composition of food ingested by blue mussels (Mytilus edulis) in the Menai Strait, where the largest mussel bed in the United Kingdom lies, hydrodynamic observations with organic carbon and nitrogen biochemical analysis were conducted. This strait is characterized by a narrow channel and wide tidal flats with large tidal mixing that influences the distribution of particulate organic matter (POM), which is food formussels. The maximum velocities of the tidal currents were estimated to be 0.5–1.0 m s-1 during northeastward flow and 0.6–1.3 m s-1 during southwestward flow. The residual current was southwestward and the water flux was estimated to be 510 m3 s-1. Field observations indicate that the inflow of pelagic phytoplankton into the strait mainly occurred in the northern region of the strait. Resuspended benthic primary production, however, also causes higher chlorophyll-a concentration in the central region of the strait near the mussel bed and its contribution to mussel growth was estimated to be 22%–50%. The concentrations of chlorophyll-a and particulate organic carbon indicated that the POM in the strait mainly originated from detritus. Benthic microalgae is, however, an important factor to understand the total primary production in the strait. The consumption of the primary producers was estimated to be approximately 6.3 t C day-1. In the phytoplankton community, pelagic and thycopelagic (living in both pelagic and benthic environments) species comprised 59.3%–77.2% and 12.8%–40.7% of the cells, respectively. The primary production by resuspended benthic species in the Liverpool Bay region was considerably larger than that in the Menai Strait region. As a conclusion, theMenai Strait is an area with complex hydrodynamic conditions causing horizontal advection and resuspension of both pelagic and benthic phytoplankton, and this complex would cause the most suitable condition for mussel production.
ONTOGENETIC VARIATION IN THE NUTRIENT STOICHIOMETRY OF JUVENILE FISH

ONTOGENETIC VARIATION IN THE NUTRIENT STOICHIOMETRY OF JUVENILE FISH by Kelsea Nicole Downs Most stoichiometric models and empirical studies to date do not take into account the ontogenetic shifts that may occur in the stoichiometry of animal bodies. To gain a better understanding of when and where ontogenetic shifts are occurring we studied the interspecific ontogenetic variation in body stoichiometry of ten different fish species from six different families. We measured the chemical composition of fish bodies including Carbon (C), Nitrogen (N), phosphorus (P), calcium (Ca) and ribonucleic acid (RNA) from embryo stage and over the course of early development. We found evidence that fish elemental stoichiometry varies over development and that there are differences across species. The results of our study based on exploring body elemental changes through time support the findings of other studies indicating that fish do not follow strict species-specific elemental homeostasis during ontogeny. ONTOGENETIC VARIATION IN THE NUTRIENT STOICHIOMETRY OF JUVENILE FISH
Diet and Feeding Behavior of the Horned Guan (Oreophasis derbianus) In Mexico

ABSTRACT. — The Horned Guan (Oreophasis derbianus) is endemic to humid montane forests of southern Mexico and Guatemala. This species is considered endangered because of their small populations, the loss and fragmentation of habitat, illegal trade, and overexploitation by subsistence hunters. We update information about the species' diet and foraging behavior by integrating the results generated during two and a half decades of research on the Horned Guan's ecology at the El Triunfo Biosphere Reserve, in Chiapas, Mexico, with additional published information compiled from other areas. Based on nearly 450 hrs of direct observations of free-ranging guans and 530 discrete feeding events, we found that during the breeding season Horned Guans feed primarily on fruits from six species of plants and leaves from one species. Horned Guans were not observed eating animal matter, corroborating its specialized frugivore-folivore habits. Our study increases the known plant taxa found in the Horned Guan's diet in El Triunfo from 40 to 63 (Supplemental Material), and globally to 101 species (Supplemental Material). For 48 taxa in El Triunfo, only fruits were consumed, while for eleven taxa consumption was restricted to leaves, and to flowers for one species; for four taxa both fruits and leaves were consumed. We found significant differences between males and females in the location of foraging on trees and diet composition. Young birds are fed fruits of Citharexylum mocinnii and leaves of Solanum appendiculatum by their mothers, both of which are rare in the diet of adult males. The conservation of the Horned Guan requires the long-term protection of suitable habitat that maintains the plant species important in their diet.