Miracle-dz/UniFAR-FTUs huggingface dataset:
Examination of the SigC regulon and cobalamin biosynthesis in Mycobacterium tuberculosis

The causative agent of tuberculosis (TB), Mycobacterium tuberculosis, remains a leading cause of morbidity and mortality, claiming ~2 million lives annually. The current live-attenuated vaccine protects against meningeal TB in children, but protection against pulmonary TB varies from 0-80% among post-adolescents. Understanding the mechanisms by which M. tuberculosis adapts to successfully reside and cause disease in the host is vital for rational design of therapeutics, vaccines, and diagnostics. In M. tuberculosis, a transcription initiation protein, sigma factor C (SigC), is a known virulence factor in murine and guinea pig TB infection models. However, no phenotypes in vitro have been reported. How SigC is regulated and how it aids the pathogen in vivo is unknown. In this study, the regulon of genes controlled by SigC was examined. Use of M. tuberculosis strains either lacking or overexpressing the sigC gene has revealed a role for SigC in trace metal acquisition. Use of medium deficient in trace metals resulted in a growth defect by a sigC mutant and will aid future studies to explore the regulation of SigC. This sigC mutant was confirmed to be attenuated in immune-compromised mice. The genomic location of the monocystronic sigC gene within a cluster of potential cobalamin biosynthesis genes led to our interest in cobalamin production. Cobalamins, such as vitamin B12, function as cofactors in various metabolic processes. While studies over fifty years ago reported vitamin B12 synthesis by mycobacteria, recent studies suggest that it is not made by M. tuberculosis. To investigate this discrepancy, production of cobalamin in mycobacteria was re-examined. Interestingly, B12 was not detected in any of the species that cause tuberculosis in mammals, but was produced in all other species tested. The presence of a full complement of cobalamin biosynthetic genes in M. tuberculosis suggests this pathogen produces the cofactor, but not under the conditions assayed. Differences in acquisition of trace metals for cobalamin synthesis by mammalian versus environmental mycobacteria or limitations of the detection methods utilized may account for the observed differences. Research is underway in the laboratory to test these hypotheses. INDEX WORDS: Mycobacterium tuberculosis, Vaccine, Sigma factor, Virulence, Gene regulation, Metals, Metal acquisition, Carbon metabolism, Vitamin B12, Cobalamin EXAMINATION OF THE SIGC REGULON AND COBALAMIN BIOSYNTHESIS IN MYCOBACTERIUM TUBERCULOSIS
Expression of a1-Adrenergic receptors on immune cells during inflammation

The immune system is a complex network of interacting cells and proteins that are constantly protecting the host from pathogens. Lymphoid and myeloid cells are the cellular mediators of the immune system, and the functions of these cells are partly controlled by the nervous system, however the mechanisms are not understood. The sympathetic nervous system may play a role through a family of receptors called adrenergic receptors (AR). Adrenergic receptors are G-protein coupled receptors that mediate the actions of adrenaline and noradrenaline. These receptors are spilt into the a- and b- subtypes, which can be further divided into subtypes. While b-ARs have been well-studied, less is known about a-ARs and their roles in immune regulation. The a-ARs can be divided into the a1- and a2 - subtypes: this project focussed on the a1-ARs as there is evidence to suggest that they play a role in inflammatory diseases. However, relatively little is known about which immune cell types express a1-ARs, and how they vary during inflammation. The major Aim of this project was to examine the expression of a1-ARs on lymphoid and myeloid cells in mouse spleen and establish whether simulating an acute inflammatory response (bacterial lipopolysaccharide: LPS) in splenocytes would alter the protein expression of a1-ARs. Protocols were optimised for the multi-parameter labelling and analysis of mouse spleen lymphoid and myeloid cells by flow cytometry, and the optimisation of specific a1-AR surface protein staining using BODIPY-prazosin. Normal mouse lymphoid and myeloid populations were found to express varying levels of -ARs, and that all except plasmacytoid dendritic cells (pDC) showed an unexpected reduction in a1-AR protein expression after exposure to LPS in vitro. The results of this project provide preliminary evidence that except for pDC, lymphoid and myeloid cell populations within the spleen undergo downregulation of a1 -ARs during an acute inflammatory response.
Best-practice language learning online: a state-of-the-art review

Many metaphors have been used to describe the Internet or the World Wide Web, the most rehearsed being the Information Superhighway. This, however, immediately gives the impression that their major function is to make information highly accessible and to provide it very quickly. While this function has an important role in education, it is only one of many elements in a broad spectrum of considerations which need to be orchestrated carefully in the quest for best practice in online language learning. Bateson's (1977)* metaphor of the orchestra seems, indeed, to be much more fitting. An orchestra going through the process of learning a new piece with the ultimate goal of turning out a public performance is a useful analogy for the experience which. a group of students and their teacher might share in an excellent online learning and teaching endeavour. A good conductor will facilitate and guide the enterprise, allowing players singly and in groups to shape the interpretation, and ultimately share ownership of the creation. Successful musicians will be intrinsically motivated, in tune with each other, prepared to work hard and open to new ways of reaching the desired goal, constantly updating their skills at both micro and macro levels. Their instruments will be of the best quality, finely tuned, highly reliable and supported by specialists, and the surrounding acoustics will be impeccable.
The effect of butyrate-supplemented total parenteral nutrition on muc2 mRNA and goblet cell chemotypes in a short bowel syndrome neonatal piglet model

Background: Compromised barrier function and bacterial translocation are common complications of short bowel syndrome (SBS) and parenteral nutrition (PN). Although mucins help prevent intestinal bacteria translocation, total mucin production has been shown to decrease during PN infusion. Butyrate administration may be a mucin fortifying strategy as it has been shown to increase mucin production in vivo and ex vivo. Objective: We tested the hypothesis that infusion of TPN supplemented with 9 mM butyrate will enhance protective goblet cell chemotypes in the small intestine, specifically sulfomucins, that enhancement of protective goblet cell chemotypes in the SCFA-supplemented group will be observed, since this group also contains 9 mM butyrate, that butyrate-supplemented TPN will have a greater effect on the small intestine than the large intestine, while butyrate supplementation at 60 mM will have a greater effect on the large intestine than the small intestine. We also hypothesize that muc2 mRNA abundance will increase in the small intestine with butyrate and SCFAsupplemented TPN infusion, whereas colonic muc2 mRNA abundance will increase in the colon with 60 mM butyrate administration. Methods: Forty-eight hour old piglets underwent 80% proximal jejunuoileal resection and were randomized to one of four groups: control total parenteral nutrition (TPN), TPN supplemented with 60 mM SCFA (36 mM acetate, 15 mM propionate, and 9 mM butyrate; SCFA), 9 mM butyrate (9Bu) or 60 mM butyrate (60Bu). Animals were further randomized to an acute (12 hour) or chronic (72 hour) time point. muc2 mRNA abundance, total goblet cell number, and total sulfomucin, sialomucin, acidomucin, and neutral mucin goblet cell numbers were ascertained. Results: Sulfomucin chemotypes were increased in the jejunal villi of the 9Bu group compared to control (treatment main effect, p=0.047). Acidomucin chemotypes in ileal crypts were greater in the 60Bu group than the control group (treatment main effect, p=0.038). In the colonic crypts, SCFA
ON FOOD AND FEEDING OF LARVAE OF THE AMERICAN OYSTER, C. VIRGINICA

1. None of the 13 species of marine bacteria tested to date was utilized as food by oyster larvae.2. Five species of flagellates, Dicrateria inornata, Chromulina pleiades, Isochrysis galbana, Hemiselmis rufescens and Pyramimonas grossii, were utilized as food by oyster larvae, while another, an unclassified chrysomonad, in addition to the three flagellates previously reported, was not.3. Chlorella sp. was not utilized as food by young oyster larvae but was utilized during later larval stages.4. None of the combinations of foods tried gave any evidence of providing a more balanced diet or more rapid larval growth than could be obtained by feeding equivalent quantities of a single food. The effects of all foods tested, including Chlorella, are additive.5. When equal numbers of cells are fed, different species of flagellates induce different rates of growth of oyster larvae.6. Species of flagellates also differ in the number of cells needed to induce the maximum rate of growth of oyster larvae.7. The maximum.
Evaluation of SWAT Applicability to Simulate Soil Erosion at Highland Agricultural Lands

The Doam watershed is located at alpine areas and the annual average precipitation, including snow accumulation, is significant higher than other areas. Thus, pollutant laden runoff and sediment discharge from the alpine agricultural fields are causing water quality degradation at the Doam watershed. To estimate soil erosion from the agricultural fields, the Universal Soil Loss Equation (USLE) has been widely used because of its simplicity to use. In the early spring at the Doam watershed, the stream flow increases because of snow melt, which results in erosion of loosened soil experiencing freezing and thaw during the winter. Also, extremely torrential rainfall, such as the typhoons 'RUSA' in 2002 and 'MAEMI' in 2003, caused significant amounts of soil erosion and sediment at the Doam watershed. However, the USLE model cannot simulate impacts on soil erosion of freezing and thaw of the soil. It cannot estimate sediment yield from a single torrential rainfall event. Also, it cannot simulate temporal changes in USLE input parameters. Thus, the Soil and Water Assessment Tool (SWAT) model was investigated for its applicability to estimate soil erosion at the Doam watershed, instead of the widely used USLE model. The SWAT hydrology and erosion/sediment components were validated after calibration of the hydrologic component. The R and Nash-Sutcliffe coefficient values are higher enough, thus it is found the SWAT model can be efficiently used to simulate hydrology and sediment yield at the Doam watershed. The effects of snow melt on SWAT estimated stream flow and sediment were investigated using long-term precipitation and temperature data at the Doam watershed. It was found significant amount of flow and sediment in the spring are contributed by melting snow accumulated during the winter. Two typhoons in 2002 and 2003, MAEMI and RUSA, caused 33% and 22% of total sediment yields at the Doam watershed, respectively. Thus, it is recommended that the SWAT model, capable of simulating snow melt, sediment yield from a single storm event, and long-term weather data, needs to be used in estimating soil erosion at alpine agricultural areas to develop successful soil erosion management instead of the USLE.
Computational analysis of next generation sequencing data : from transcription start sites in bacteria to human non-coding RNAS

The advent of next generation sequencing (NGS) technologies has revolutionized the field of molecular biology by providing a wealth of sequence data. “Transcriptomics”, which aims to identify and annotate the complete set of RNA molecules transcribed from a genome, is one of the main applications of these high-throughput methods. Special attention has been paid in determining the exact position of the 5’ ends of RNA transcripts, the transcription start sites (TSSs), and subsequently in identifying the regulatory motifs that are ultimately responsible for governing gene expression. Recently, a novel experimental approach termed dRNA-seq has emerged which enables TSS identification in prokaryotic genomes at a genome-wide scale. While the experimental procedure has reached a point of maturity, the computational downstream analysis of dRNA-seq data is still in its infancy. Analysis of dRNA-seq data was previously done manually, a tedious task that is prone to errors and biases. In order to automate this process we developed a computational tool for accurate and systematic analysis of dRNA-seq data to identify the TSSs genome-wide. In particular, we used a Bayesian framework for TSS calling and a Hidden Markov Model to infer the canonical motifs in the promoter regions of TSSs in order to further capture TSSs that show low evidence of expression. In a second contribution, we exploited the power of next generation sequencing to identify and characterize the expression and processing mechanisms of snoRNAs. SnoRNAs are a particular class of non-protein coding RNAs whose main function is post-transcriptional modification of other non-protein coding RNAs. SnoRNAs carry out their function as part of ribonucleoprotein complexes (RNPs). In order to gain insights into these protein-RNA interactions, we used a technique called PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) that allows the identification of protein-RNA contacts at nucleotide resolution. Using PAR-CLIP data, we were able to demonstrate that snoRNAs undergo precise processing and that many loci in the human genome generate snoRNA-like transcripts whose evolutionary conservation and expression are considerably lower than currently catalogued snoRNAs. Finally, we set out to use small RNA-seq data from the ENCODE project to construct a comprehensive catalog of genomic loci that give rise to snoRNAs. In addition we expanded the current catalog of human snoRNAs and studied the plasticity of snoRNA expression across different cell types. Our analysis confirmed prior observations that several snoRNAs show cell type specific expression, mainly in neurons. A more striking observation was that snoRNA expression appears to be strongly dysregulated in cancers which could lead to the identification of novel biomarkers.
Effect of clutch size on incubation persistence in male Wilson's phalaropes (Phalaropus tricolor)

ABSTRACr. -The effect of clutch size on incubation persistence of male Wilson's Phalaropes (Phalaropus tricolor) was studied over two breeding seasons in south-central Saskatchewan. The Wilson's Phalarope is a "sex-role-reversed" shorebird in which only males incubate and provide parental care. The breeding season is long enough to allow for renesting but not for the rearing of more than one brood per male. Barring secondary mating strategies, the total annual reproduction of a male is limited by the size of its clutch. Females lay determinate clutches of four eggs. By determining the minimum clutch size necessary for male incubation persistence, we demonstrated that males alter their reproductive effort in response to clutch size, and we identified the minimum potential annual reproduction for males necessary to maintain this unusual mating system. Clutch-size reductions led to an increased frequency of abandonment inversely proportional to the number of eggs remaining in the clutch. The timing of egg loss also was critical. Among males with clutches reduced to one egg or reduced to two eggs early in the incubation cycle, all but one abandoned incubation. Among males with clutches reduced to two eggs late in incubation or three eggs early, an intermediate proportion abandoned incubation. All but one male with three eggs late in incubation or a full, four-egg clutch continued to incubate. Experimentally increasing clutch sizes by two eggs over the normal four-egg clutch led to rapid nest failure. This suggests that the determinate, four-egg clutch of females is not suboptimal for males and that nest parasitism of two eggs by females has little potential benefit as an alternative reproductive tactic. Received 24 February 1992, accepted 22 November 1992.
Foliar morphology and physiology of Sequoia sempervirens

iii ACKNOWLEDGEMENTS.v TABLE OF CONTENTS . vi LIST OF TABLES . viii LIST OF FIGURES.ix INTRODUCTION.1 Morphology.1 Turgor Pressure and Water Potential.3 Physiology.4 METHODS . 7 Study Site and Species.7 Sampling Protocol . 8 Morphological Measurements.9 Gas exchange Measurements . 10 Light response curves . 11 A-Ci response curves . 12 Statistical Analysis . 14
FEEDBACK DIFFERENTIAL SYSTEMS: APPROXIMATE AND LIMITING TRAJECTORIES

A ”feedback differential system” is defined as a (generally discontinuous) parameterized differential inclusion (in particular, differential equation), that usually appears in the description of the complete solution of an optimal control problem or a differential game. In this article one obtains certain invariant characterizations of the uniform limits of two types of approximate trajectories: the well-known ”Euler polygonal lines” and the less known ”Isaacs approximate trajectories” suggested by the natural assumption of the discrete (step-by-step) ”action” of a player in optimal control and differential games. The main results state that under very general hypotheses on the data, the limiting Euler and, respectively, Isaacs-Krassovskii-Subbotin trajectories are Carathéodory solutions of two distinct associated differential inclusions defined by corresponding ”u.s.c.convexified” limits of the original orientor fields. In particular, one provides a counter-example of a ”conjecture” in Krassovskii and Subbotin(1974) and one gives a complete proof of the correct variant of this conjecture.
Effective Observation and Critical Reflection (A Snaphot).

What do pre-service teachers learn from their observation stint during school experience attachment? This paper will present insights into the cognitive contents of the pre-service teachers’ reflection log. Preliminary analyses revealed that different cultures and pedagogical practices were observed to be in operation in different school contexts. This paper will discuss the teacher trainees’ perspectives of their experiential learning and critical reflection during their school experience. It will present a retrospective analysis of the subjects’ reflective thoughts on the following aspects that they had observed: their cooperating teachers’ practices in class, the running of the school organization, setting their own goals and the charting of their own development as trainee teachers.
EVALUATION OF MEMBRANE BIOREACTOR TECHNOLOGY AND DESALTING MEMBRANES FOR WASTEWATER REUSE

The City of Rio Rancho and MWH have recently completed a pilot-testing program to evaluate MBR technology followed by reverse osmosis (RO) membranes during operation on municipal wastewater. The pilot testing program is part of an overall water reuse plan being implemented by the City of Rio Rancho, NM to conserve water supplies through recycling of wastewater currently being discharged to the Rio Grande River. The primary objective of this study was to demonstrate that MBR technology can meet local water reuse goals for commercial, landscape irrigation, and industrial uses, as well as surface water discharge requirements. In addition, the study focused on demonstrating that RO membranes can operate on MBR effluent to produce high quality purified water for groundwater recharge. Lastly the study evaluated the ability of MBR and RO processes to remove selected emerging contaminants, including endocrine disrupting compounds (EDCs) and pharmaceuticals and personal care products (PPCPs). In order to meet project objectives pilot system consisting of MBR/RO was operated over a 6-month period. During this time a water quality sampling plan was implemented to cover a wide range of inorganic and organic contaminates regulated under the Safe Drinking Water Act and New Mexico Water Quality Commission. Results from the study showed that MBR consistently produced a high water quality suitable for industrial and irrigation non-potable uses and provided a robust pretreatment to RO. In addition, product water from the overall treatment train met all federal and state regulations. Lastly most EDC and PPCP compounds were removed through the MBR/RO process to concentration levels below analytical detection.
The Art of Making Change Initiatives Stick

Too many managers are burned out on strategic change. They have lived through the scenario in which the CEO announces a bold initiative designed to dramatically lift performance. The initiative calls for sweeping changes in the company's processes, systems and culture; it unfolds with great fanfare and large resource investments. Later, managers look back and wonder what went wrong. Even when there are some short-term gains, it's common for the organization to slip back into old ways of doing things. Employees typically dismiss the initiative as just another "flavor of the month" exercise. This article argues for a system that enables change initiatives to stick. The authors use a detailed case study (a large clothing retailer disguised as "Apparelizm Corp.") to demonstrate what it takes to produce sustainable changes in processes, behavior or performance. The study uncovered four critical processes - chartering, learning, mobilizing and realigning - that pave the way for successful institutionalization of a strategic change initiative. The elements rely much more on an understanding of the mix of task-related, emotional and behavioral factors than is fashionable in today's metrics-driven environment. The article also highlights the study's divergence from conventional wisdom about programmatic change. Whereas most prior research has emphasized early articulation of a sense of urgency, the authors found that managers need to set in motion a series of processes right at the start if widespread changes are to stick. They must reshape the organizational structure, demonstrate that processes are fair and legitimate, and employ a range of open approaches to engage people's emotions if they want strategic initiatives to become more than the latest flavor of the month.
Inactivation and Attachment of Listeria monocytogenes on Beef Muscle Treated with Lactic Acid and Selected Bacteriocins.

Cubical pieces (1 cm3) of aseptically obtained beef muscle were treated with lactic acid (2%), nisin (4 × 104 IU/ml) and pediocin PO2 (a bacteriocin produced by Pediococcus acidilactici PO2; 3.2 × 103 arbitrary units/ml). Treated meat was immersed for 1 min in a cell suspension of a mixture of two strains of Listeria monocytogenes and then stored for 48 h at 4°C. Meat cubes were analyzed immediately after immersion in the cell suspension, then after 1, 24, and 48 h of storage. Count of L. monocytogenes per cube and percentage of attached cells were determined. Data indicated that the antimicrobial agents significantly (p = 0.05) decreased the count of L. monocytogenes during the 48-h storage by 1.7, 1.1, and 0.6 log10 CFU/6 cm2 of meat surface for lactic acid, nisin, and pediocin PO2 treatments, respectively. Lactic acid on the meat surface had an immediate and also a delayed listericidal action, but bacteriocins only inhibited L. monocytogenes immediately, and had little or no delayed antilisterial effect. The percentage of Listeria cell attached to the beef muscle significantly (p = 0.05) increased in the presence of lactic acid, but the value did not change significantly or slightly decreased in the presence of nisin and pediocin PO2, respectively.
Yeast flocculation : understanding cell surface structure-function relationships in industrial yeast strains

II DEDICATION. III AUTHOR’S DECLARATION . IV CERTIFICATE . V ACKNOWLEDGEMENTS. VI UADPERMISSION TO COPY. VII ACRONYMS/ABBREVIATIONS/SYMBOLS. VIII LIST OF FIGURES. XVIII LIST OF TABLES. XXII