Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution of genome-wide gene regulation in the budding yeast cell-division cycle

EVOLUTION OF GENOME-WIDE GENE REGULATION IN THE BUDDING YEAST CELL-DIVISION CYCLE Daniel F. Simola Junhyong Kim Genome-wide regulation of gene expression involves a dynamic epigenetic structure which generates an organism’s life-cycle. Although changes in gene expression during development have broad effects on many basic phenomena including cell growth, differentiation, morphogenesis, and disease progression, the evolutionary forces influencing gene expression dynamics and gene regulation remain largely unknown, due to the nature of gene expression as a polygenic, quantitative trait. Moreover, gene expression is regulated differentially over time, so evolutionary forces may be influenced by developmental context. To advance the understanding of evolution in the context of the life-cycle, the architecture of gene expression timing control and its influence on expression dynamics must be revealed. This dissertation presents two experimental investigations of the evolution of genes and related structural regions and time-dependent gene expression, using the budding yeasts Saccharomyces cerevisiae and Saccharomyces paradoxus and their mitotic cell-division vii cycle as model organism and life-cycle. Comparative methodologies were employed to analyze genome-wide patterns of genetic and phenotypic diversity within and between species. Analysis of several dozen yeast genomes reveals a dominant evolutionary mode of purifying selection. Despite limited genetic variability, differences in transcriptional regulation appear to contribute predominantly to interspecies divergence, and altered posttranscriptional regulation of ribosomal genes may have altered the timing of each species’ transition from vegetative growth to reproduction, a classic life-history trait. In addition, natural variation in genome-wide gene expression was measured as a time-series through the mitotic cell-division cycle of 10 yeast lines, including one outgroup species. Despite levels of variation consistent with strong stabilizing selection, transcriptome coexpression dynamics have diverged significantly within and between species. A model involving timing pattern changes explains 61% of the between-genome variation in expression dynamics, suggesting that the major mode of transcriptome evolution involves changes in timing (heterochrony) rather than changes in levels (heterometry) of expression. Analysis of heterochrony patterns suggests that timing control is organized into distinct and dynamicallyautonomous modules. Divergence in expression dynamics may be explained by pleiotropic changes in modular timing control. Genome-wide gene regulation may utilize a general architecture comprised of multiple discrete event timelines, whose superposition could produce combinatorial complexity in timing patterns.
CARBOHYDRATE-DEFICIENT TRANSFERRIN AND GAMMA- GLUTAMYL TRANSPEPTIDASE-MARKERS OF EXCESSIVE ALCOHOL CONSUMPTION

Carbohydrate-deficient transferrin (CDT) represents an important instrument for the evaluation process of alcohol consumption. But there is not a consensus on its use in the routine practice. The objective of this study was to compare carbohydrate-deficient transferrin and gamma- glutamyl transpeptidase (GGT) assays for the evaluation of alcohol consumption. 165 patients (100 males and 65 females) were included in this study. Patients were divided into five categories according to alcohol consumption: category 1 included non-weaned patients drinking more than 30 g/day for women and more than 50 g/day for men, category 2 included relapse patients, category 3 included moderate drinkers, category 4 included patients weaned less than one month, and category 5 included patients weaned more than one month. A specifically standardized questionnaire was used. Blood samples were drawn at the alcohol-cure outpatient centre. Samples were drawn at the first consultation and later as prescribed depending on the clinical situation. Sensitivity of CDT varied, depending on patient category, from 36% to 96% versus 45% to 70% for GGT. Specificity of CDT varied from 72% to 90% versus 21% to 61% for GGT. This study shows that carbohydrate-deficient transferrin is more accurate in predicting alcohol consumption compared with gamma-glutamyl transpeptidase in alcoholic patients evaluation.
A Tagging Study on Yellowtail Kingfish (Seriola Lalandi) and Samson Fish (S. Hippos) in South Australian Waters

Summary Wild yellowtail kingfish (Seriola lalandi Valenciennes, 1833) and Samson fish (S. hippos Günther, 1876) were tagged with nylon-headed, single-barbed dart tags between December 1, 2004 and December 31, 2006 in Spencer Gulf and offshore from the west coast of Eyre Peninsula, South Australia. Two-hundred and forty-one S. lalandi and 73 S. hippos were tagged. Twenty-four S. lalandi were recaptured and the maximum distance between capture points was 130 km and the maximum time at liberty was 442 days. Two S. hippos were recaptured, of which one was at liberty for a maximum of 378 days. Both S. hippos were recaptured at the original capture site. Recapture results indicate that large S. lalandi remain in, or return to, northern Spencer Gulf. This region may be important for aggregations of large, reproductively mature S. lalandi. One large S. lalandi tagged at Port Augusta was recaptured near Fitzgerald Bay, indicating that wild fish may move past S. lalandi sea-cage farms in this region. This course of movement may provide opportunities for disease and parasite interactions between wild and farmed fish. An additional outcome of this research was the residual impact that it has had on sustainable fishing practices in South Australia with increased recreational fisher participation in the tag and release of S. lalandi and S. hippos.
The blaCTX-M-12 gene's genetic environmnt in Klebsiella pneumoniae hospital isolates

Genes from CTX-M-1 group have been detected with great frequency in Colombia in intrahospital infection-causing Klebsiella pneumoniae isolates. Knowledge regarding the genetic factors favouring such genes’ dissemination amongst bacterial species is an important issue for resistance control blaCTX-M-12 gene-carrying plasmids were identified in this study in 21 clinical K. pneumoniae isolates. Antibiotic resis tance transfer was evaluated by mating. Integrons, insertion sequences and other genetic elements were detected by plasmid DNA amplification using polymerase chain reaction ( PCR). The relationship between the blaCTX-M-12 gene and other genetic elements was determined by PCR analysis. The blaCTX-M-12 gene was
Microbial adaptations to temperature modulates carbon use efficiencies

Decomposer microorganisms hold a key position in biogeochemical cycles and temperature is one of the dominant environmental factors that determine biological rates in ecosystems. The influence of temperature on microbial processes is therefore crucial for understanding soil carbon (C) dynamics. Also, our ability to understand the temperature relationship and adaptability of microbial processes in soil, is a prerequisite for improving modelling of the dynamics of the terrestrial ecosystem.
An Overlapping Generations Model of Taxpayer Bailouts of Banks

The paper constructs an overlapping generations model to evaluate how different bank rescue plans affect banks’ risk-taking incentives. For a non-competitive banking industry, we find bailout with tax imposed on the old generation or equity bail-in to be efficient policies in the sense that they implement socially optimal risk-taking. In a competitive banking sector, no-bailout implements the socially-optimal risk-taking. Bailout policies financed by a tax imposed on the young generation always induce excessive risk-taking.
Polyphenol content and antioxidant capacity of eggplant skin

Eggplant (Solanum melongena) represents one of the best dietary sources of biologically active polyphenolic compounds. Polyphenolic‐rich extracts from darkly colored grape and cranberry fruit skins are known to inhibit the oxidative modification of low density lipoprotein (LDL) lipids and proteins. Dark purple skinned Blackbell and Millionaire eggplant varieties were grown under controlled agricultural conditions after which the skin polyphenolic content was extracted. Skin extracts contained phenolic acids (3‐caffeoylquinic acid, 4‐caffeoylquinic acid,5‐caffeoylqunic, dihydroxy cinnamoyl amide, caffeic acid conjugates), flavonols (myricetin‐3‐galactoside, quercitin‐3‐glucoside, quercitin‐3‐rhamanoside), in addition to anthocyanins, and proanthocyanidins whose specific identity were not determined. Polyphenolic extracts from all sources potently delayed the cupric ion‐mediated lag‐time for LDL lipid oxidation (234 nm), the formation of thiobarbituric acid reactive substances, and protected Apo‐B100 proteins against oxidative modification. Future studies of the biological activities of eggplant polyphenolics may improve eggplant cultivar selection for nutritional health benefits.
The role of host and viral proteins in intra- and inter-cellular trafficking of geminiviruses☆

Geminiviruses are insect-transmitted ssDNA plant viruses that reproduce in intact host nuclei. To be infectious, the viral DNA must be able to overcome numerous transport barriers. Upon entrance into a host cell, the virus enlists host machinery to facilitate both its transport through the complex lattice-like structure of the cytoplasm to the nucleus and its uptake into the nucleus through the nuclear pore complex (NPC). Following replication and transcription of its genome, the infectious form of the virus exploits host transport machinery together with virus-encoded movement proteins (MP) to egress from the nucleus and to be transported through the cytoplasm to, and through, the virus-modified plasmodesmata (Pd). Here we describe viral and plant proteins involved in these processes and present a model summarising our accumulated knowledge.
Review: microsatellite markers in amphibian conservation genetics

Recent technical advances allow straightforward access to genetic information directly drawn from DNA. The present article highlights the suitability of high variation molecular genetic markers, such as microsatellites, for studies relevant to amphibian conservation. Molecular markers appear particularly useful for i) measuring local gene flow and migration, ii) assigning individuals to their most likely population of origin, iii) measuring effective population size through the between-generation comparison of allele frequencies, and iv) detecting past demographic bottlenecks through allele frequency distortions. We demonstrate the use of some newly developed analytical tools on newt (Triturus sp.) microsatellite data, discuss practical aspects of using microsatellites for amphibians, and outline potential future research directions.
A Tale of Two Programs: Broadening Participation of Underrepresented Students in STEM at Loyola Marymount University

This paper highlights two programs that successfully support underrepresented students in STEM disciplines at Loyola Marymount University (LMU). ACCESS (A Community Committed to Excellence in Scientific Scholarship) is a program that focuses on academics and critical thinking skills, which provides a threeweek residential component for incoming students and continued mentoring during their first year in college. The LMU McNair Scholars Program is one of over 150 McNair Scholars Program sites federally-funded by the U.S. Department of Education and has the overarching goal of increasing number of graduate degrees awarded to students from underrepresented segments of society. For both ACCESS and McNair, we give an overview of each program and detail about components of the programs that have led to success. In addition, we specifically address the rewards and challenges when providing mentorship at multiple levels.
Strigolactones: A New Class of Plant Hormones with Multifaceted Roles

Strigolactones (SLs) are terpenoid lactones produced mainly in plant roots and initially identified as seed germination stimulants for parasitic weeds. In 2005, they were described also as boosters of hyphal branching in arbuscular mycorrhizal fungi, and thereby as promoters of arbuscular mycorrhizal symbiosis. In 2008, they emerged as a new class of plant hormones controlling plant architecture through repression of shoot branching. Since then, several new roles were discovered for SLs: in the adaptive responses to a number of environmental stimuli (including light, osmotic stress, interaction with pathogens and nodulating bacteria), and in several aspects of plant development (including seed germination for nonparasitic plants, hypocotyl elongation, reproduction, leaf senescence and nodulation). The biosynthetic and perception/transduction systems of SLs are being elucidated, and the first mechanistic models presented. Key Concepts: Strigolactones are the key nutrient allocators regulating plant development at the interface between plants, beneficial and detrimental (micro)organisms, and abiotic factors. Strigolactones induce hyphal branching in AM fungi and facilitate the establishment of symbiosis. Strigolactones inhibit shoot branching. Strigolactones affect root architecture and root development depending on nutrients availability. Synthetic SLs (analogues and mimics) are used in pharmacological applications to plants and fungi to decipher the structure–activity relationship. Structure–activity relationship (SAR): Different structures are tested for bioactivity in order to pinpoint which part of the molecule is essential for bioactivity and which can be considered only ‘decoration’. Keywords: strigolactones; plant hormones; plant development; symbiosis; AM fungi; parasitic plants; shoot branching; hyphal branching; biofertilisers
Crystalline amino acids and nitrogen emission.

Reductions in dietary protein level and supplementation with certain crystalline amino acids is a well-established method of formulating diets to achieve a more ideal amino acid pattern and to reduce nitrogen excretion. Up to 35% reduction in nitrogen excretion may be achieved by supplementing pig diets with lysine, methionine, threonine, and tryptophan. In broiler nutrition, 41% less N was excreted on feeding diets with 153 g CP per kg supplemented with amino acids
REVIEW: Questionnaires in ecology: a review of past use and recommendations for best practice

1. Questionnaires, or social surveys, are used increasingly as a means of collecting data in ecology. We present a critical review of their use and give recommendations for good practice. 2. We searched for papers in which questionnaires were used in 57 ecological academic journals, published over the period 1991–2003 inclusive. This provided a total sample size of 168 questionnaires from 127 papers published in 22 academic journals. 3. Most questionnaires were carried out in North America and western Europe, and addressed species-level issues, principally focusing on mammals. The majority were concerned with impacts of species and/or their conservation, and just under half with human–wildlife interactions. 4. Postal survey was the method used most frequently to carry out the questionnaires, followed by in-person interviews. Some questionnaires were conducted by telephone, and none was web-based. 5. Most questionnaires were concerned with obtaining factual information or perceptions of facts. Ground-truthing (independent verification of the facts) was carried out in less than 10% of questionnaires. 6. The mean (± SE) sample size (number of respondents) per questionnaire was 1422 ± 261 and the average (± SE) response rate was 63 ± 3%. These figures varied widely depending on the methods used to conduct the questionnaire. 7. The analysis of data was mostly descriptive. Simple univariate methods were the most frequently used statistical tools, and data from a third of questionnaires were not subjected to any analysis beyond simple descriptions of the results. 8. Synthesis and applications. We provide recommendations for best practice in the future use of questionnaires in ecology, as follows: (i) the definition of the target population, any hypotheses to be tested and procedures for the selection of participants should be clearly documented; (ii) questionnaires should be piloted prior to their use; (iii) the sample size should be sufficient for the statistical analysis; (iv) the rationale for the choice of survey method should be clearly stated; (v) the number of non-respondents should be minimized; (vi) the question and answer format should be kept as simple as possible; (vii) the structure of the questionnaire and the data emerging from it should be unambiguously shown in any publication; (viii) bias arising from non-response should be quantified; (ix) the accuracy of data should be assessed by ground-truthing where relevant; (x) the analysis of potentially interrelated data should be done by means of modelling. Researchers should also consider whether alternative, interpretative methods, such as in-depth interviews or participatory approaches, may be more appropriate, for example where the focus is on elucidating motivations or perceptions rather than testing factual hypotheses.
Identifying Molecular Mechanisms and Cellular Origins of Cancers of the Nervous System

Cancers of the nervous system are the most common type of solid tumors among children. They are a heterogeneous population of benign and malignant tumors that growth within the central or peripheral nervous system. The molecular mechanisms governing onset and progression, and the cellular origins of these cancers remain intense areas of research. We created mouse models that develop multiple tumors in both the central and peripheral nervous systems. We deleted Pten and activated K-ras using Cre-lox technology driven by the mouse GFAP promoter. Our models develop benign neurofibromas that progress to malignant peripheral nerve sheath tumors, optic nerve tumors, and malignant brain gliomas. We find that loss of the PTEN tumor suppressor is critical in the onset and progression of these tumors. In addition, we show that 18F-fluorodeoxyglucose positron emission tomography can distinguish peripheral nerve sheath tumors as benign or malignant, and is an effective modality to monitortherapeutic response to multi-kinase inhibitors. Furthermore, we establish a new cell-of-origin in malignant brain gliomas. We deleted Pten and activated K-ras in adult neural stem cells of the mouse brain and performed developmental tracing analysis to determine where in the neurogenic niche tumors initiated. We show that gliomas initiate from a region called the subcallosal zone (SCZ), the caudal extension of the subventricular zone (SVZ). We find that progenitors in the SCZ transform prior to those in the SVZ, and that the cellular compositions in each region are uniquely affected by our genetic manipulation. These results reveal a critical role of the SCZ in gliomagenesis. As such, these studies define a novel molecular mechanism in the progression of peripheral nerve sheath tumors, and propose a new cell-of-origin in brain gliomas.
Properties of Cholesterol Dissimilation by Rhodococcus equi.

The identification of serum cholesterol as a risk factor in the development of coronary heart disease has resulted in attempts to reduce dietary cholesterol intake. As a result, the removal of cholesterol from food products has become a challenging research objective. We report here the loss of 40% of the cholesterol found in egg yolk preparations following treatment with sonicated extracts of Rhodococcus equi . Extracts of R. equi 21107 and R. equi 33706 removed 3.33% and 3.09% of the cholesterol from egg yolk per min per mg of crude enzyme protein, respectively. Incubation of fresh cream with R. equi 33706 extracts resulted in only a 2.4% reduction in cholesterol content (rate of reduction: 0.35% cholesterol per min per mg of protein). Cholesterol degradation by R. equi 33706 had an optimum temperature of 40°C and an optimum pH of 8.0, and there was no apparent requirement for divalent metal ions. Approximately 44% of enzyme activity was lost after a 60 min exposure at 60°C. Thin layer chromatographic analysis of cholesterol degradation products revealed only a few steroid-like compounds, primarily 4-cholesten-3-one and 1,4-cholestadiene-3-one.
Regulation of transforming growth factor beta-1 signalling in the renal proximal tubular epithelial cells

The data presented shows that IL-1beta has a biphasic effect on PTC TGF-beta signalling, with early NF-kappaB-mediated inhibition and delayed sensitization via an autocrine IL-6 loop, and possibly also via an autocrine IL-6 loop, and possibly also via a switch from NF Kappa B p52/p50 heterodimer to p50/p50 homodimer formation. Secondly, the data indicates that BMP-7 prevents TGF-beta1-mediated loss of the transcriptional repressor SnoN and hence specifically limits Smad3 DNA binding, altering the balance of transcriptional responses to TGF-beta1 in PTC
The Role of Resource Predictability in the Metapopulation Dynamics of Insects

Govindan, Byju N. Ph.D., Purdue University, December 2013. The Role of Resource Predictability in the Metapopulation Dynamics of Insects. Major Professor: Robert K. Swihart. The metapopulation paradigm has emerged as an important tool to understand the dynamics of species living in fragmented landscapes. In this dissertation, I investigate the unpredictable nature of resource availability for species living in human-dominated heterogeneous and dynamic landscapes in the context of its consequences for long-term regional persistence of species. In particular, I test theoretical advancements in metapopulation ecology following a two-pronged approach via experiments in the lab and observations in the field using insects. In chapter 1, I introduce the concept of metapopulation ecology in the context of its relevance for dynamics of species living in fragmented landscapes and describe my objectives. In chapter 2, I investigate the main and interactive effects of resource availability (constant vs. diminishing), patch connectivity (low vs. high), and dynamics of patch configuration (static vs. dynamic) on landscape and patch level colonization, extinction and abundance of red flour beetles (Tribolium castaneum) as well as metapopulation stability. Patch connectivity and configuration interacted to influence beetle abundance and stability, with intermediate connectivity and patch dynamics leading to greater persistence. In chapter 3, I test