Mitochondrial inheritance during a parasexual cycle in {\it Fusarium oxysporum\/} forma specialis {\it cubense\/}

Fusarium oxysporum is a diverse, asexual fungal species composed of both saprophytic and pathogenic members. The destructive phytopathogens are classified into formae speciales based on the host species and into vegetative compatibility groups (VCGs) based on the ability of two individuals to form heterokaryons. Parasexuality, a non-sexual mode of genetic exchange unique to some fungi has been demonstrated in the laboratory in Fusarium oxysporum f. sp. cubense (FOC). The goals of this dissertation were threefold: to ascertain whether mitochondrial (mt) markers can distinguish race differences in FOC; to determine genetic relatedness of VCGs in FOC based on a mt marker; and to discover the mode of mt inheritance during a parasexual cycle.^ Band patterns produced by electrophoresis of Hae III digested genomic DNA indicated that VCG differences, not race, could be discerned by mtDNA analysis. Primers were designed to amplify a mt intergenic locus which served as a molecular marker to screen 55 strains of FOC in 16 VCGs using both single strand conformational polymorphism and DNA sequencing. Based on homogeneity of the locus, strains were assigned to seven mitotypes, a classification unit which I introduced and found informative for grouping related VCGs.^ To determine the mode of mt inheritance during a parasexual cycle, strains in different mitotypes were paired. Mitochondrial inheritance in all hybrid progeny was found to be uniparental. I speculated that if a parasexual cycle occurs in nature there would be greater variation in the nuclear genome than the mt. This could produce multiple VCGs within a mitotype, a phenomenon observed in FOC. Based on these data, I concluded that parasexuality in nature may contribute to the diversity observed in Fusarium oxysporum. ^

Effects of cooperative and individual integrated learning system on attitudes and achievement in mathematics

This study compares the effects of cooperative delivery (CD) and individual delivery (ID) of integrated learning system (ILS) instruction in mathematics on achievement, attitudes and behaviors in adult (16-21 yrs.) high school students (grades 9-13). The study was conducted in an urban adult high school in Miami-Dade County Public Schools using a pre-test/post-test design. Achievement was measured using the Test of Adult Basic Education (TABE) by CTB MC-Graw-Hill and Compass Learning. An attitudinal survey measured attitudes towards mathematics, the computer-related lessons, and attitudes toward group activities. Behavior was assessed using computer lab observations. ^ Two-way analyses of variance (ANOVA) were conducted on achievement (TABE and Compass) by group and time (pre and post). A one-way ANOVA was conducted on the overall attitude by group on the five components (i.e., content mathematics, delivery/computers, cooperative, partners, and self efficacy) and a one-way ANOVA was conducted on the on-task behavior by group. ^ The results of the study revealed that CD and ID students working on mathematics activities delivered by the ILS performed similarly on achievement tests of the TABE. The CD-ILS students had significantly better overall mathematics attitudes than the ID-ILS students and the ID-ILS group was on-task significantly more than the CD-ILS group. This study concludes that regularity and period of time over which the ILS is used may prove to be important variables although there were insufficient data to fully investigate the impact of models of use. Additionally, a minimum amount of time-on-system is necessary before gains can become apparent in innumeracy and increasing exposure to the system may have beneficial effects on learning. ^

Effects of ocean acidification on embryonic respiration and development of a temperate wrasse living along a natural CO2 gradient

Volcanic CO2 seeps provide opportunities to investigate the effects of ocean acidification on organisms in the wild. To understand the influence of increasing CO2 concentrations on the metabolic rate (oxygen consumption) and the development of ocellated wrasse early life stages, we ran two field experiments, collecting embryos from nesting sites with different partial pressures of CO2 [pCO2; ambient (400 µatm) and high (800-1000 µatm)] and reciprocally transplanting embryos from ambient- to high-CO2 sites for 30 h. Ocellated wrasse offspring brooded in different CO2 conditions had similar responses, but after transplanting portions of nests to the high-CO2 site, embryos from parents that spawned in ambient conditions had higher metabolic rates. Although metabolic phenotypic plasticity may show a positive response to high CO2, it often comes at a cost, in this case as a smaller size at hatching. This can have adverse effects because smaller larvae often exhibit a lower survival in the wild. However, the adverse effects of increased CO2 on metabolism and development did not occur when embryos from the high-CO2 nesting site were exposed to ambient conditions, suggesting that offspring from the high-CO2 nesting site could be resilient to a wider range of pCO2 values than those belonging to the site with present-day pCO2 levels. Our study identifies a crucial need to increase the number of studies dealing with these processes under global change trajectories and to expand these to naturally high-CO2 environments, in order to assess further the adaptive plasticity mechanism that encompasses non-genetic inheritance (epigenetics) through parental exposure and other downstream consequences, such as survival of larvae.

(Table 3) Grain size composition of Holocene deposits from the Kara Sea

A new generalized schematic map of distribution of recent sediments within Eurasian Arctic shelves is considered. The sediments have accumulated as a result of interaction of various factors and processes specific to high latitudes. They include input of terrigenous material by modern glaciers, ice transport, thermal abrasion, sedimentation controlled by many years of ice cover, and others. Characteristic regularity is marked over Arctic shelves: in seas with heavier ice cover, the most fine-grained deposits are distributed, they contain minimum amount of coarse-grained ice rafted debris; in seas with lighter ice cover mosaic distribution of various types of sediments is observed. Composition of surface sediments from the Arctic shelves corresponds to a relatively cool stage of the modern interglacial period. In the 21-st century a new warming is expected.

Corrigendum to “Regularity for Stably Projectionless, Simple C ∗ -Algebras”

Peer reviewed

Dissecting the Functional Impacts of Non-Coding Genetic Variation

A large proportion of the variation in traits between individuals can be attributed to variation in the nucleotide sequence of the genome. The most commonly studied traits in human genetics are related to disease and disease susceptibility. Although scientists have identified genetic causes for over 4,000 monogenic diseases, the underlying mechanisms of many highly prevalent multifactorial inheritance disorders such as diabetes, obesity, and cardiovascular disease remain largely unknown. Identifying genetic mechanisms for complex traits has been challenging because most of the variants are located outside of protein-coding regions, and determining the effects of such non-coding variants remains difficult. In this dissertation, I evaluate the hypothesis that such non-coding variants contribute to human traits and diseases by altering the regulation of genes rather than the sequence of those genes. I will specifically focus on studies to determine the functional impacts of genetic variation associated with two related complex traits: gestational hyperglycemia and fetal adiposity. At the genomic locus associated with maternal hyperglycemia, we found that genetic variation in regulatory elements altered the expression of the HKDC1 gene. Furthermore, we demonstrated that HKDC1 phosphorylates glucose in vitro and in vivo, thus demonstrating that HKDC1 is a fifth human hexokinase gene. At the fetal-adiposity associated locus, we identified variants that likely alter VEPH1 expression in preadipocytes during differentiation. To make such studies of regulatory variation high-throughput and routine, we developed POP-STARR, a novel high throughput reporter assay that can empirically measure the effects of regulatory variants directly from patient DNA. By combining targeted genome capture technologies with STARR-seq, we assayed thousands of haplotypes from 760 individuals in a single experiment. We subsequently used POP-STARR to identify three key features of regulatory variants: that regulatory variants typically have weak effects on gene expression; that the effects of regulatory variants are often coordinated with respect to disease-risk, suggesting a general mechanism by which the weak effects can together have phenotypic impact; and that nucleotide transversions have larger impacts on enhancer activity than transitions. Together, the findings presented here demonstrate successful strategies for determining the regulatory mechanisms underlying genetic associations with human traits and diseases, and value of doing so for driving novel biological discovery.

Three Essays on the Effects of Donor Supplied Contraceptives on Fertility, Usage, and Attitudes

After the 2012 London Summit on Family Planning, there have been major strides in advancing the family planning agenda for low and middle-income countries worldwide. Much of the existing infrastructure and funding for family planning access is in the form of supplying free contraceptives to countries. While the average yearly value of donations since 2000 was over 170 million dollars for contraceptives procured for developing countries, an ongoing debate in the empirical literature is whether increases in contraceptive access and supply drive declines in fertility (UNFPA 2014).

This dissertation explores the fertility and behavioral effects of an increase in contraceptive supply donated to Zambia. Zambia, a high-fertility developing country, receives over 80 percent of its contraceptives from multilateral donors and aid agencies. Most contraceptives are donated and provided to women for free at government clinics (DELIVER 2015). I chose Zambia as a case study to measure the relationship between contraceptive supply and fertility because of two donor-driven events that led to an increase in both the quantity and frequency of contraceptives starting in 2008 (UNFPA 2014). Donations increased because donors and the Zambian government started a systematic method of forecasting contraceptive need on December 2007, and the Mexico City Policy was lifted in January 2009.

In Chapter 1, I investigate whether a large change in quantity and frequency of donated contraceptives affected fertility, using available data on contraceptive donations to Zambia, and birth records from the 2007 and 2013 Demographic and Health Surveys. I use a difference-in-difference framework to estimate the fertility effects of a supply chain improvement program that started in 2011, and was designed to ensure more regularity of contraceptive supply. The increase in total contraceptive supply after the Mexico City Policy was rescinded is associated with a 12 percent reduction in fertility relative to the before period, after controlling for demographic characteristics and time controls. There is evidence that a supply chain improvement program led to significant fertility declines for regions that received the program after the Mexico City Policy was rescinded.

In Chapter 2, I explore the effects of the large increase in donated contraceptives on modern contraceptive uptake. According to the 2007 and 2013 Demographic and Health Surveys, there was a dramatic increase in current use of injectables, implants, and IUDs. Simultaneously, declines occurred in usage of condoms, lactational amenorrhea method (LAM), and traditional methods. In this chapter, I estimate the effect of the increase in donations on uptake, composition of contraceptive usage, and usage of methods based on distance to contraceptive access points. The results show the post-2007 period is associated with an increase in usage of injectables and the pill among women living further away from access points.

In Chapter 3, I explore attitudes towards the contraceptive supply system, and identify areas for improvement, based on qualitative interviews with 14 experts and 61 Zambian users and non-users of contraceptives. The interviews uncover systemic barriers that prevent women from consistently accessing methods, and individual barriers that exacerbate the deficiencies in supply chain procedures. I find that 39 out of 61 women interviewed, both users and non-users, had personal experiences with stock out. The qualitative results suggest that the increase in contraceptives brought to the country after 2007 may have not contributed to as large of a decline in fertility because of bottlenecks in the supply chain, and problems in maintaining stock levels at clinics. I end the chapter with a series of four recommendations for improvements in the supply chain going forward, in light of recent commitments by the Zambian government during the 2012 London Summit on Family Planning.

Smear slide analysis of sediment core GeoB5836-2

Laminated sediments spanning the last 20,000 years (though not continuously) in the Shaban Deep, a brine-filled basin in the northern Red Sea, were analyzed microscopically and with backscattered electron imagery in order to determine laminae composition with emphasis on the diatomaceous component. Based on this detailed study, we present schematic models to propose paleoflux scenarios for laminae formation at different time-slices. The investigated core (GeoB 5836-2; 26°12.61'N, 35°21.56'E; water depth 1475 m) shows light and dark alternating laminae that are easily distinguishable in the mid-Holocene and at the end of the deglaciation (13-15 ka) period. Light layers are mainly composed of coccoliths, terrigenous material and diatom fragments, while dark layers consist almost exclusively of diatom frustules (monospecific or mixed assemblages). The regularity in the occurrence of coccolith/diatom couplets points to an annual deposition cycle where contrasting seasons and associated plankton blooms are represented (diatoms-fall/winter deposition, coccoliths-summer signal). We propose that, for the past ~15,000 years, the laminations represent two-season annual varves. Strong dissolution of carbonate, with the concomitant loss of the coccolith-rich layer in sediments older than 15 ka, prevents us from presenting a schematic model of annual deposition. However, the diatomaceous component reveals a marked switch in species composition between Last Glacial Maximum (LGM) sediments (dominated by Chaetoceros resting spores) and sediments somewhat younger (18-19 ka; dominated by Rhizosolenia). We propose that different diatom assemblages reflect changing conditions in stratification in the northern Red Sea: Strong stratification conditions, such as during two meltwater pulses at 14.5 and 11.4 ka, are reflected in the sediment by Rhizosolenia layers, while Chaetoceros-dominated assemblages represent deep convection conditions.

Age determination of the Vendian intrusions in the polar Urals

The Precambrian basement beneath the Pechora Basin of northern Russia is known from deep (up to approx. 4.5 km) drill holes to be largely composed of Neoproterozoic successions, variously deformed and metamorphosed and intruded by magmatic suites of Vendian age. Presented here are new single- zircon, Pb-evaporation (Kober method) ages from eight intrusions across the Izhma, Pechora and Bolshezemel'skaya Zones, all from below the Lower Ordovician (locally Middle Cambrian) unconformity. The majority of the intrusions (six) yield remarkably similar ages of 550-560 Ma, apparently dating a widespread pulse of late- to post-tectonic magmatism. An early Vendian granite (618 Ma) has been identified in the northeasternmost region (Bolshezemel'skaya zone) and a Devonian granodiorite (380 Ma) in the Pechora Zone, where mid to late Palaeozoic magmatism has been previously reported. Evidence of inheritance in the zircon populations suggests the presence of Mesoproterozoic crust beneath the Neoproterozoic complexes.

In situ d18O and Mg/Ca analyses of ODP Site 143-865 samples

We report d18O and minor element (Mg/Ca, Sr/Ca) data acquired by high-resolution, in situ secondary ion mass spectrometry (SIMS) from planktic foraminiferal shells and 100-500 µm sized diagenetic crystallites recovered from a deep-sea record (ODP Site 865) of the Paleocene-Eocene thermal maximum (PETM). The d18O of crystallites (~1.2 per mil Pee Dee Belemnite (PDB)) is ~4.8 per mil higher than that of planktic foraminiferal calcite (-3.6 per mil PDB), while crystallite Mg/Ca and Sr/Ca ratios are slightly higher and substantially lower than in planktic foraminiferal calcite, respectively. The focused stratigraphic distribution of the crystallites signals an association with PETM conditions; hence, we attribute their formation to early diagenesis initially sourced by seafloor dissolution (burndown) ensued by reprecipitation at higher carbonate saturation. The Mg/Ca ratios of the crystallites are an order of magnitude lower than those predicted by inorganic precipitation experiments, which may reflect a degree of inheritance from "donor" phases of biogenic calcite that underwent solution in the sediment column. In addition, SIMS d18O and electron microprobe Mg/Ca analyses that were taken within a planktic foraminiferal shell yield parallel increases along traverses that coincide with muricae blades on the chamber wall. The parallel d18O and Mg/Ca increases indicate a diagenetic origin for the blades, but their d18O value (-0.5 per mil PDB) is lower than that of crystallites suggesting that these two phases of diagenetic carbonate formed at different times. Finally, we posit that elevated levels of early diagenesis acted in concert with sediment mixing and carbonate dissolution to attenuate the d18O decrease signaling PETM warming in "whole-shell" records published for Site 865.

Who is in charge? An L2 Discourse Intonation Study on Four Prosodic Parameters to Exert the Pragmatic Function of Dominance and Control in the Context of L2 Non-specialist Public Speaking

This paper reports the findings from a study of the learning of English intonation by Spanish speakers within the discourse mode of L2 oral presentation. The purpose of this experiment is, firstly, to compare four prosodic parameters before and after an L2 discourse intonation training programme and, secondly, to confirm whether subjects, after the aforementioned L2 discourse intonation training, are able to match the form of these four prosodic parameters to the discourse-pragmatic function of dominance and control. The study designed the instructions and tasks to create the oral and written corpora and Brazil’s Pronunciation for Advanced Learners of English was adapted for the pedagogical aims of the present study. The learners’ pre- and post-tasks were acoustically analysed and a pre / post- questionnaire design was applied to interpret the acoustic analysis. Results indicate most of the subjects acquired a wider choice of the four prosodic parameters partly due to the prosodically-annotated transcripts that were developed throughout the L2 discourse intonation course. Conversely, qualitative and quantitative data reveal most subjects failed to match the forms to their appropriate pragmatic functions to express dominance and control in an L2 oral presentation.

Point-and-shoot: rapid quantitative detection methods for on-site food fraud analysis – moving out of the laboratory and into the food supply chain

Major food adulteration and contamination events occur with alarming regularity and are known to be episodic, with the question being not if but when another large-scale food safety/integrity incident will occur. Indeed, the challenges of maintaining food security are now internationally recognised. The ever increasing scale and complexity of food supply networks can lead to them becoming significantly more vulnerable to fraud and contamination, and potentially dysfunctional. This can make the task of deciding which analytical methods are more suitable to collect and analyse (bio)chemical data within complex food supply chains, at targeted points of vulnerability, that much more challenging. It is evident that those working within and associated with the food industry are seeking rapid, user-friendly methods to detect food fraud and contamination, and rapid/high-throughput screening methods for the analysis of food in general. In addition to being robust and reproducible, these methods should be portable and ideally handheld and/or remote sensor devices, that can be taken to or be positioned on/at-line at points of vulnerability along complex food supply networks and require a minimum amount of background training to acquire information rich data rapidly (ergo point-and-shoot). Here we briefly discuss a range of spectrometry and spectroscopy based approaches, many of which are commercially available, as well as other methods currently under development. We discuss a future perspective of how this range of detection methods in the growing sensor portfolio, along with developments in computational and information sciences such as predictive computing and the Internet of Things, will together form systems- and technology-based approaches that significantly reduce the areas of vulnerability to food crime within food supply chains. As food fraud is a problem of systems and therefore requires systems level solutions and thinking.

Trivial Jensen measures without regularity

In this note we construct Swiss cheeses X such that R(X) is non-regular but such that R(X) has no non-trivial Jensen measures. We also construct a non-regular uniform algebra with compact, metrizable character space such that every point of the character space is a peak point.