Miracle-dz/UniFAR-FTUs huggingface dataset:
Control of Chironomid Midges in Recreational Lakes

Several commonly available and experimental insecticides were evaluated for control of chironomid midge larvae, Chironomus spp. , Proclaideus spp. , and Tanytarsus spp. in 2 recreational lakes. In Lake Calabasas, where the bottom has a thin layer of mud on a surface of cement, standard midge larvicides such as Abate® ( O, O -dimethyl phosphorothioate O, O -diester with 4,4′-thiodiphenol) and fenthion proved highly effective. Fenthion at 0.5 Ib per surface acre controlled the larvae for more than 7 weeks. At this rate of application very slight mortality of the mosquito fish Gambusia affinis (Baird & Girard) was observed. Abate at 0.75 pounds per acre controlled the midges for about 4–5 weeks and caused slight mortality of the fish. Dursban® ( O, O -diethyl O -(3,5,6-trichloro-2-pyridyl) phosphorothioate) at the rate of 0.2 Ib/acre yielded long-lasting control of midge larvae, the suppression lasting for almost 5 months. In Westlake (about 10 miles from Lake Calabasas), with a natural bottom, where small portions were treated, fenthion at 0.5 lb/acre yielded little or no control of the midge larvae. Abate at 0.5 pounds per acre produced similar results. Carbaryl at 0.5 and 1.0 pounds per acre yielded good control, but its longevity was for only 2-3 weeks. Dursban insecticide applied as granules or sprays at 0.2 pounds per acre yielded excellent control of midge larvae. The granular formulations produced better and longer-lasting larval control than an emulsifiable concentrate formulation. The latter formulation at 0.2 lb/acre or higher rate caused slight kill of blugill, Lepomis macrochirus Rafinesque; largemouth bass, Micropterus salmoides Lacepede; and black crappie, Pornoxis nigromaculatus (Le Sueur) in the lake. No mortality of fish was observed in plots treated with a granular formulation of Dursban at the same rate.
TRIM24 orchestrates metabolic reprogramming and EMT in Breast Cancer

vi Table of contents . viii List of Figures . xi List of Tables . xiii List of Appendices . xiv List of Abbreviations . xv Chapter 1: Introduction . 2 1.1 Breast cancer: . 2 1.2 Cancer metastasis and EMT: . 4 1.3 Cancer cells and deregulated metabolism: . 8 1.4 TRIM family and TRIM24: . 11 Chapter 2: Materials and methods . 23 2.1 Cell culture . 23 2.2 Cell proliferation, soft agar colony formation, and cell-cycle analysis . 24 2.3 Generation of stable cells . 24 2.4 Quantitative real-time PCR (qRT-PCR) . 25 2.5 nCounter analysis . 25 2.6 Immunoblotting and Immunohistochemistry . 26
Antigen and superantigen presentation as defined by the MHCII-accessory proteins and associated-peptides

MHCII molecules expose a weave of antigens, which send survival or activation signals to T lymphocytes. The ongoing process of peptide binding to the MHC class II groove implicates three accessory molecules: the invariant chain, DM and DO. The invariant chain folds and directs the MHCII molecules to the endosomal pathway. Then, DM exchanges the CLIP peptide, which is a remnant of the degraded invariant chain, for peptides of better affinity. Expressed in highly specialized antigen presenting cells, DO competes with MHCII molecules for DM binding and favors the presentation of receptor-internalized antigens. Altogether, these molecules exhibit potential immunomodulatory properties that can be exploited to increase the potency of peptide vaccines. DO requires DM for maturation and to exit the ER. Interestingly, it is possible to monitor this interaction through a conformation change on DOβ that is recognized by the Mags.DO5 monoclonal antibody. Using Mags.DO5, we showed that DM stabilizes the interactions between the DO α1 and β1 chains and that DM influences DO folding in the ER. Thus, the Mags.DO5+ conformation correlates with DO egress from the ER. To further evaluate this conformation change, directed evolution was applied to DO. Of the 41 unique mutants obtained, 25% were localized at the DM-DO binding interface and 12% are at the solvent-exposed β1 domain, which is thought to be the Mags.DO5 epitope. In addition, I used the library to test the ability of HLA-DO to inhibit HLA-DM and sorted for the amount of CLIP. Interestingly, most of the mutants showed a decrease inhibitory effect, supporting the notion that the intrinsic instability of DO is a required for its function. Finally, these results support the model in which DO competes against classical MHCII molecules by sequestering DM chaperone’s function. MHCII molecules are also characterized by their ability to present superantigens, a group of bacterial or viral toxins that coerces MHCII-TCR binding in a less promiscuous fashion than what is observed in a canonical setting. While the mechanism of how bacterial superantigens form trimeric complexes with TCR and MHCII is well understood, the mouse mammary tumor virus superantigens (vSAG) are poorly defined. In the absence of a crystal structure, I chose a functional approach to examine the relation between vSAG, MHCII and TCR with the goal of uncovering the overall trimolecular architecture. I showed that TCR concomitantly binds both the MHCII α chain and the vSAG and that TCR-MHCII docking is almost canonical when coerced by vSAGs. Because many peptides may be tolerated in the MHCII groove, the pressure exerted by vSAG seems to tweak conventional TCR-MHCII interactions. Furthermore, my results demonstrate that vSAG binding to MHCII molecules is conformation-dependent and abrogated by the CLIP amino-terminal residues extending outside the peptide-binding groove. In addition, they also suggest that vSAGs cross-link adjacent MHCIIs and activate T cells via a TGXY motif.
Influence of inorganic and organic nitrogen on enzymes of nitrogen assimilation and growth in tomato seedlings

Summary Recent evidence suggests that agricultural and horticultural crops may be able to take up significant quantities of dissolved organic nitrogen (DON). Our aims were to determine the effects of supplying different forms of N on growth and on the activities of N-assimilatory enzymes in tomato. Two genotypes of tomato were grown in sterile hydroponic culture without N (control), with NO3– or NH4+ (3 mM), or with organic-N in the form of glycine (1.5, 3.0, or 6.0 mM). The results showed that biomass production and N-contents were similar in both genotypes when supplied with NO3– or with glycine, and that this growth was much greater than in plants supplied with NH4+ alone, or without added N. In addition, the production of plant biomass was positively correlated with the concentration of glycine-N used; however, the magnitude of the response was genotype-dependent. The form of N supplied also significantly affected the activities of several key N-assimilatory enzymes in roots and shoots. For example, addition of glycine increased the activities of NADH-glutamate dehydrogenase (NADH-GDH), glutamate oxaloacetate transaminase (GOT), and glutamate pyruvate transaminase (GPT) in roots, compared with the NO3– or NH4+ treatments. Our results clearly demonstrate the intrinsic ability of tomato plants to use DON as a sole source of N. Further studies to investigate the functional significance of DON in horticultural systems under non-sterile conditions are therefore warranted.
Characterization of the Dicistroviridae intergenic region internal ribosome entry site

The IRES found in the intergenic (IGR) region of viruses belonging to the Dicistroviridae family is remarkable for its ability to bind directly to the ribosome with high affinity and initiate translation without the requirement for any initiation factors by mimicking a P/E hybrid tRNA. Here, we have conducted an in-depth biochemical characterization of the CrPV IGR IRES. We have found that the L1.1 region of the IRES is responsible for 80S assembly and reading frame maintenance, and may play an additional role downstream of ribosome binding. Additional studies on the modularity of the IRES showed that the two domains of the IGR IRES work independently, but in concert with one another to manipulate the ribosome. We then addressed the question of how the IGR IRES recruits ribosomes during periods of cellular stress, when inactive 80S couples accumulate in the cell. Here, we found that the IRES is able to bind directly to eEF2-associated 80S couples, providing a rationale as to how the IRES remains translated during these periods. Finally, we developed a new in vitro translation system to assess the functionality of specialized ribosomes, and used this system and the IGR IRES in order to ask questions about the pathology of dyskeratosis congenita. Though divergent from other viral IRESs, the simplicity of this tRNA-like IRES serves as a powerful model for understanding IRES functions in general, the role of tRNA/ribosome interactions that occur normally during translation, and how these processes are linked to the greater context of the cell.
Circadian rhythms in Synechococcus elongatus PCC 7942: insights into the regulatory mechanisms of the cyanobacterial clock system

Circadian Rhythms in Synechococcus elongatus PCC 7942: Insights into the Regulatory Mechanisms of the Cyanobacterial Clock System. (August 2006) Shannon Rose Mackey, B.A., The University of Texas at Austin Chair of Advisory Committee: Dr. Susan S. Golden Circadian rhythms of behavior have been well characterized in organisms including mammals, plants, insects, fungi, and photosynthetic bacteria. Cyanobacteria, such as the unicellular Synechococcus elongatus PCC 7942, display near 24-h circadian rhythms of gene expression. These rhythms persist in the absence of external cues, can be reset by the same stimuli to which they entrain, and are relatively insensitive to changes in ambient temperature within their physiological range. Key components have been identified as belonging to the central oscillator that comprises the timekeeping units, output pathways that relay temporal information to clock-controlled processes, and input pathways that synchronize the oscillator with local time. The emerging model of the cyanobacterial clock depicts the internal timekeeping elements KaiA, KaiB, and KaiC interacting with one another to form a large, multimeric complex that assembles and disassembles over the course of a day. Information is sent into and out of the oscillator via signal transduction pathways that include proteins involved in bacterial twocomponent systems. The research presented in this dissertation explores the regulatory mechanisms that exist at each level of the clock system. New components were iii
Precarious Work and less well paid? Wage Differential between Regular and Temporary Contract Workers in India

News reports, press anecdotes and serious research articles concerning Asia in general and India in particular have identified wealth, income and wage inequalities that have caused tremendous social and economic concern as they pose a serious challenge for social and political cohesion and have significant costs for economic growth (The Hindu 2017; Chakravarty 2016; Ramaswamy 2008). The raging debate over the rising trend in wage inequality is, of course, not a new phenomenon. It has been resurrected in the public discourse after the publication of Global Wage Report 2016-17 by ILO in December, 2016. According to this report, in India, the highestpaid top 10 per cent of income groups receive almost 43 per cent of total wages paid to all employees; whereas, the lowest-paid bottom 50 per cent income groups receives only 17 per cent of total wages paid to all employees. Moreover, the report also observes the following three important dimensions of growing wage inequalities in India1) the upper tail of wage distribution is highly concentrated in the hands of 1 per cent highest-paid income groups, who enjoys more than 33 times share of total wages than the bottom 10 per cent lowest-paid income groups; 2) women workers earns 33 times less than the male workers; and finally, 3) the persistence of wage inequality within the enterprise and industrial sector is driving the total wage inequality (ILO 2016). It is evident that the large sections of the workforce have not been able to reap the dividends of high growth of Indian economy and have been excluded from the developmental outcomes. The last observation of the report brings out the important aspects of rising wage inequality, which has not received the detailed attention it deserves. Different bases of inequities could be identified such as gender; skill-based, social and religious identities and so on which have received some attention in the inequities and discrimination literature (see Karan 2008; Ramaswamy 2008; Madeshwaran and Attewell 2007). But in the post-liberalization period an important flexi-type employment has been intensified greatly in terms of its numbers and width of operation and in some cases staggering numbers , i.e. temporary contract labour. Temporary contract labour cut across all labour market and social markers such as gender, caste, religion, and immigrant and so on. The inequality of income between these workers and their directly-employed counterparts has not been studied in detail in the literature so far. This article examines the determinants and trends in rising wage inequality between two categories of workforce across different labour regulation regimes.
Transgenic study of chloroplast translocon gene regulation in Arabidopsis thaliana.

The majority of chloroplast proteins is encoded by the nuclear genome and must be accurately imported to plastids. The translocons on the outer envelope and inner envelope membrane of chloroplasts (the Toc and Tic proteins) play key roles in the machinery of protein import into the chloroplast. Among the Toc and Tic components identified in Arabidopsis thaliana, atToc33 and atToc34 are paralogous to pea psToc34 and play important roles in pre-protein recognition. The expression of atToc33 and atToc34 genes must be properly regulated, or their gene products will not be correctly integrated to their destination to allow their function. To reveal the regulatory mechanism of atToc33 and atToc34 gene expression, transgenes containing various lengths of the upstream regulatory sequences of atToc33 and atToc34 genes and GUS coding sequence were transferred into wild-type Arabidopsis. We found that the atToc33 and atToc34 genes are preferentially expressed in leaves and roots, respectively. Furthermore, atToc34 is also regulated in an age-dependent manner. Finally, the leader intron in the 5' UTR of both genes up-regulates the gene expression in mature plants. These data suggest that atToc33 and atToc34 play distinct roles in chloroplast function and development.
Carbon dioxide flux and metabolic processes of a coral reef, Okinawa

This study investigates carbon dioxide flux associated with calcification, photosynthesis and respiration on a coral reef atoll near Okinawa, Japan. Metabolic activity and nutrient concentrations were routinely measured at three study sites: (1) on the reef flat, (2) in the lagoon, and (3) 10 50 m off the reef. Sampling was undertaken during low spring tide events, when the atoll was temporarily emerged over five periods in 1993-95. Two of the five sampling periods included both day and night sampling. Alkalinity, Dissolved Inorganic Carbon (DIC), Dissolved Oxygen (DO) anti pH varied slightly among sampling periods, however there were no differences in the range of variation. Compared to the lagoon and open waters, the reef flat had significantly lower alkalinity and DIC, and significantly higher DO and pH during the day. ΔDIC reached a maximum shortly before sunrise and was closely coupled with total alkalinity over the diel cycle. Rates of net organic carbon production and calcification for the reef flat were estimated at 12 mmol m -2 h -1 and 9 mmol m -2 h -1 , respectively, although calcification was low (i.e., under the detection limit) at night. The respiration rate of the reef flat was approximately 6 mmol m -2 h 1 . A comparison of CO 2 released by calcification and net organic production indicates that this reef flat acted as a sink for atmospheric carbon dioxide in the daytime, but acted as a source at night, and that the net CO 2 diel budget was almost equally balanced.
Mammals of the Savannah River Site

This book is designed to be used as a field guide, reference book, bibliography, and introduction to the basic biology and ecology of the 54 mammal species that currently or potentially exist on or near the Savannah River Site (SRS). For 50 of these species, we present basic descriptions, distinguishing morphological features, distribution and habitat preferences, food habits, reproductive biology, social behavior, ecological relationships with other species, and economic importance to man. For those species that have been studied on the SRS, we summarize the results of these studies. Keys and illustrations are provided for whole body and skull identification. A selected glossary defines technical terminology. Illustrations of tracks of the more common larger mammals will assist in field identifications. We also summarize the results of two major long-term SRS studies, ``The Forbearer Census`` and ``White-tailed Deer Studies``. A cross-indexed list of over 300 SRS publications on mammals classifies each publication by 23 categories such as habitat, reproduction, genetics, etc., and also for each mammal species. The 149 Master`s theses and Ph.D. dissertations that have been conducted at the Savannah River Ecology Laboratory are provided as additional references.
Oxygen availability and microdistribution of interstitial mesofauna in Swedish fresh-water sandy beaches

The oxygen regime of three fresh-water sandy beaches in southern and middle Sweden was investigated. Microdistribution of interstitial mesofauna was examined at the same time, and the influence of oxygen availability measured as oxygen diffusion rate (ODR) upon the microdistribution was noted. The ODR is influenced by different environmental conditions. Sudden changes in the ODR are caused by rapidly changing factors, e.g. movement of interstitial water in parts of the beach influenced by wave action. Normal diel temperature variation in the beach implies that surface ODR values, in those parts of the beach where the sand surface is wetted by waves or by capillary action, may show a diel variation. Changes in oxygen concentration of the interstitial water are gradual and therefore sudden changes in ODR caused by this factor are unlikely. Ground-water pressure, porosity of the sand and amount of detritus undergo sudden changes only at the water line. Strata of coarser sand may display higher ODR than strata of fine sand in the vicinity, owing to better drainage. No direct correlation between redox potential and ODR can be found, although strongly reducing Eh values may imply oxygen depletion. In parts of the beach where the superficial layers are moist, a strong correlation can be found between oxygen availability and mesofaunal development. In these parts moisture content, grain size and other environmental factors are often regularly distributed vertically, while a strong gradient in ODR is found, with higher values in the superficial layers. This is reflected in a strong concentration of animals in the uppermost layers. In the middle beach animals may congregate in areas where the ODR values are higher than in the surrounding layers. In this part moisture content limits the distribution of most mesofaunal groups upwards. Values of ODR reported as limiting for harpacticoid copepods are found in deeper layers of the beach without seeming to limit these animals' distribution. Pe3NoMe
Acid Phosphatase in Rice Seedlings

Acid phosphatase (EC 3. 1. 3. 2.) extracted from rice seedlings consisted of ten kinds of isozymes based on separation by polyacrylamide gel electrophoresis. One isozyme was purified through ammonium sulfate precipitation, Ultrogel gel filtration, DEAE-trisacryl chromatography and chromatofocusing. This enzyme had a high affinity to p-nitrophenyl phosphate. The molecular weight of this isozyme was around 130kD examined with FPLC and it consisted of heterodimer with molecular weight of 70kD and 62kD. The purified isozyme had a pH optimum at 5.0 and its Km (p-nitrophenyl phosphate) was 0.69 mM. Mg^(++) and Mn^(++) enhanced the activity, but heave metal ions were inhibitory. NaF and Na2MoO4 also had an inhibitory effect on the isozyme.
Sensitivity to dihydrofolate reductase inhibitors and molecular karyotypes in some plasmodium falciparum isolates in Kenya

Ten Kenyan isolates of Plasmodium falciparum were characterized by their molecular karyotype and antimalarial drug sensitivity. For chromosomal analysis pulse field gradient gel electrophoresis was used. Plasmodium falciparum isolates from malarious areas in Nyanza, Rift Valley and Coast provinces were cultivated in vitro and used for the karyotype study. The sensitivities of cultured isolates to three antifolate malarial drugs (pyrimethamine, cycloguanil and chlorcycloguanil) and sulphadoxine which is a sulphonamide were examined by the in vitro radioisotopic methods of Desjardins et al. (1979) with minor modifications. Considerable variation was found in the antimalarial drug response of the 10 parasite isolates. Among the four antimalarial drugs examined, chlorcycloguanil and cycloguanil had similar potencies. They were more potent than pyrimethamine and sulphadoxine. Sulphadoxine and pyrimethamine had similar potencies. Cycloguanil and chlorcycloguanil, which are closely related biguanides were highly correlated in their antimalarial activities. There was no correlation between the activity of the three antifolates and sulphadoxine. The isolates from the Rift Valley province showed significantly lower susceptibility to the four antimalarial drugs tested than those from the Coast and Nyanza provinces. The isolates from Coast province showed the highest susceptibility. The chromosomal bands were found to range in number from 14 to 16 and in size from 600 to 4300 kilobase pairs, and there was extensive variation in chromosome size. Two isolates had more than the constant number of chromosomes, suggesting a mixed population of parasite strains in natural malarial infections.There were inter and intraregional differences in the sizes of the chromosomes. However, there was no correlation between band size and drug sensitivity. The degree of polymorphism shown by the
Isolation and identification of protease-producing bacteria from the intertidal zone in Jeju Island, Korea

Eleven protease-producing bacteria were isolated from the organisms’ external shells and the inorganic materials collected from intertidal zone of Jeju Island, Republic of Korea. The samples were diluted serially, inoculated on Zobell agar plates with 1% skim milk and incubated at 20°C. Clear zone forming colonies were selected as protease-producing bacteria and each strain was identified based on the phylogenetic analysis with their 16S rDNA sequences. Strains JJM125, JJM129, YG47 and YG49 belong to the marine bacterial genus Pseudoalteromonas; strain JJM122 belong to the genus Microbulbifer; strains YG51, YG52, YG62 and YG63 belong to the genus Vibrio; and strain YG65 belong to genus Bacillus. Hence, the present study suggests that these protease producing bacteria could be further used to develop new varieties of protease with various biotechnological applications.