Miracle-dz/UniFAR-FTUs huggingface dataset:
The effects of disease mutations on the transcription factor Interferon Regulatory Factor 6

Van der Woude syndrome (VWS) and popliteal pterygium syndrome (PPS) are autosomal dominant disorders characterized by combinations of cleft lip and cleft palate (CLP), lip pits, skin-folds, syndactyly and oral adhesions. VWS and PPS are caused by mutations in the transcription factor Interferon regulatory factor 6 (IRF6). IRF6 belongs to a family of transcription factors that share a highly conserved DNA-binding domain (DBD) and a less conserved protein-binding domain. Mutation analysis reveals a general genotype-phenotype correlation between the distribution of mutations and the manifestation of either VWS or PPS. However, the molecular mechanisms by which these mutations affect IRF6 function are still unknown. Therefore the aim of this project was to characterize the molecular function and regulation of IRF6 and subsequently determine the effects of VWS and PPS mutations on IRF6 function. DNA binding site-selection showed that the IRF6-DBD exhibited optimal binding site selectivity for the consensus sequence AACCGAAACC/T. This sequence was used to investigate the effects of VWS and PPS mutations in the DBD. Almost all mutations abrogated DNA-binding. It was subsequently demonstrated that a VP16AD-IRF6-DBD fusion protein was able to activate transcription from a promoter containing the derived binding site. However, wildtype IRF6 was shown to be autoinhibited and compartmentalized in the cytoplasm. To determine what signals are involved in the nuclear translocation of IRF6, internal signals that facilitate nucleocytoplasmic trafficking were mapped. The cytoplasmic localization of IRF6 suggested that the identified nuclear export signal (NES) 159IQDTFPFLNI168 is constitutively active and dominant over the nuclear localization signal 5PRRVRLK11. Disruption of the NES leads to nuclear retention; however nuclear localization alone is insufficient for functional activation of IRF6. Therefore, the role of phosphorylation in the regulation of IRF6 was assessed. Five novel phosphorylation sites were identified in IRF6 at residues S47, S131, S153, S424 and T425. Phosphorylation at S424/S425 was necessary for combinatorial phosphorylation at the serine/threonine rich region to induce nuclear retention, whereas, phosphorylation in the DBD at S47 abrogates DNA-binding. The understanding of IRF6 molecular function and mechanisms of regulation provides further insight into the pathways involved in the pathogenesis of VWS and PPS.
Redescripción de "Eukoenenia hanseni" (Arachnida: Palpigradi) y descripción de una nueva especie de palpígrado de México

Eukoenenia hanseni (Silvestri, 1913) has been reported as being widely distributed in Mexico and in other countries. In this study, a multivariate analysis was used to compare two distinct geographic populations, including the type locality in Jalapa, Veracruz. Eukoenenia hanseni is redescribed based on the male holotype and additional male and female topotypes, and a new species is described, Eukoenenia chilanga sp. n. , from Mexico City. A new morphologic group, chilanga-florenciae, is proposed within the genus Eukoenenia.
Essays on Education and Labour Economics

31 Lühikokkuvõte . 33 Appendix . 37 Paper I . 37 Paper II . 55 Paper III . 69 Paper IV . 87 Curriculum vitae . 106 Elulookirjeldus . 111
Characterization of the pathogenicity and phylogeny of members of the Rhodococcus genus

approved: ______________________________________________________ Jeff H. Chang Plant pathogenic Rhodococcus species are persistent pathogens able to cause severe growth deformities on a large range of hosts. The most well studied species, R. fascians is predicted by current models to synthesize a mixture of cytokinins that act to directly perturb the hosts’ hormone balances, which results in abnormal growth. The biosynthesis and modification of cytokinins has been attributed to proteins encoded by the fas locus. The fasD gene encodes an isopentenyl transferase, a key enzyme in cytokinin biosynthesis, and is necessary for pathogenicity. In addition to fasD, fasA, putatively encoding a P450 monooxygenase, and fasF, encoding a phosphoribohydrolase, are hypothesized to be necessary for pathogenicity. The work presented in this thesis employs the use of whole genome sequences from over 20 isolates of Rhodococcus to challenge the current virulence model and develop new models. Counter to the current virulence model, our data shows R. fascians produces only one active cytokinin in a fas-dependent manner. Analysis of the genome sequences revealed a unique pathogenic isolate that lacks the fas operon. However, this isolate contains a gene predicted to encode a protein with isopentenyl transferase and phosphoribohydrolase domains, putatively capable of catalyzing and activating cytokinins, respectively. We also developed methods to generate non-polar gene deletion mutants of fasA and fasF, two key genes in the extant virulence model. Characterization of these mutants indicates fasA and fasF are not necessary for pathogenicity. Finally, we used the genome sequences from 59 Rhodococcus isolates, including the 21 genomes we sequenced, to provide a framework for resolving the Rhodococcus genus. ©Copyright by Allison L. Creason May 12, 2015 All Rights Reserved Characterization of the Pathogenicity and Phylogeny of Members of the Rhodococcus Genus. by Allison L. Creason
URINARY INCONTINENCE IN WOMEN: PRIMARY HEALTHCARE PHYSICIANS‘ KNOWLEDGE AND PRACTICE IN THE EASTERN PROVINCE, SAUDI ARABIA

Urinary incontinence (UI) in women is an awkward, often undiscussed subject, associated with anxiety, depression, social isolation and affecting quality of life. This study aimed to assess primary healthcare physicians' knowledge and practice in Saudi Arabia's Eastern Province. This cross-sectional study was conducted in primary healthcare centers of three main sectors (Dammam, Khobar and Qatif) in the Eastern Province by a self- administered survey. The sample size was 120 physicians who completed the questionnaire. Most primary healthcare physicians clearly understood UI, one-third of them routinely asked patients about UI, and about 55% of them commonly encountered UI in their practice. Lack of screening tools, unfamiliarity with available treatment algorithms, and lack of time were the most common barriers. Almost all primary care providers (95.8%) referred UI patients to secondary care. Sixty percent physicians had good overall knowledge, and 52.5% had good attitudes and practices about UI. There was no statistically signiﬁcant relationship except for job level in relation to knowledge and practice scores. Improved education and basic screening programs and treatment in primary care centers would improve UI detection and management at the primary care level.
The Flexural Strength of Wood Connection using Different Lengths of Waste Plastic Bottle as Connector

: Various types of wood processing produce wood waste beside indeed the wood products. Wood waste can be re used by joining it using wood connector, which was in this current study used waste plastic bottle by heating the plastic using a hot air gun at a certain temperature. The length of the connector could be influence to the strength of the wood connection. Therefor this study was conducted to observe the flexural strength of the wood connection using waste plastic bottle as connector in some different lengths by doing an experimental study. Thirty samples with 5x5x76 cm in dimension were prepared from five variations of the connection length that were 5, 10, 15, 20, and 25 cm. Eight samples made for each variations of length. The results indicate that the length of the connector significantly influence in the flexural strength of the wood connection. The length of the plastic connector which met the highest flexural strength was 20 cm which was reach 65.091 kg / cm2 or 7.58% of the undamaged wood or wood without connection.
Interactions of polyhalogenated aromatic hydrocarbons with thyroid hormone metabolism

Treatment of rats with different polyhalogenated aromatic hydrocarbons strongly decreases plasma T4, with little or no decrease in plasma T3. The extrathyroidal effects of TCDD on thyroid hormone turnover were studied by ip administration of a single dose of 10 ug TCDD/kg bw or vehicle (corn oil) to euthyroid (Eu) rats, thyroidectomized (Tx) rat, and Tx rats infused with 1 ug T4 (Tx+T4) or 0.4 ug T3 (Tx+T3) per 100 g bw per day by osmotic minipumps. Tx rats showed decreased plasma T4 and T3 and increased plasma TSH levels, decreased hepatic Dl and malic enzyme activities, and increased brain D2 activities. All parameters were largely restored to Eu levels in Tx+T4 rats and, except for plasma T4 and brain D2 activity, in Tx+T3 rats, validating the thyroid hormone-replaced Tx rats as models to study the peripheral effects of TCDD. Three days after TCDD administration, plasma T4 and FT4 levels were significantly reduced in Eu rats and in Tx+T4 rats, and plasma T3 was significantly reduced in Tx+T3, but not in Eu or Tx+T4 rats. Plasma TSH was not affected by TCDD in any group. Hepatic T4 UGT activity was induced approximately 5-fold by TCDD while T3 UGT activity was only increased by about 20% (p=NS) in the different groups. TCDD produced an insignificant decrease in liver Dl activity in Tx rats and an insignificant increase in brain D2 activity in Tx rats and hormone-replaced Tx rats. Hepatic malic enzyme activity was significantly increased by TCDD in all groups, except Tx rats. These results strongly suggest that the thyroid hormonedecreasing effects of TCDD are predominantly extrathyroidal and mediated by the marked induction of hepatic T4 UGT activity. based on A. Gerlienke Schuur, Franklin M. Boekhorst, Abraham Brouwer, and Theo J. Visser (1997). Extrathyroidal effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin on thyroid hormone turnover in male Sprague-Dawley rats. Endocrinology 128, 3727-3734.
The Mucin-Alginate Interplay: Investigating the Rheological Impact of Alginates and Their Influence on Particle Mobility

Mucus is a hydrogel that covers epithelial cells and acts as an intermediary between the exterior and interior surfaces of the human body. It is complex and diverse, comprised of various compounds and serves as a selective barrier to pathogens, nutrients and administered substances. It is therefore important to circumvent or penetrate this barrier to increase drug bioavailability. The most important constituent of mucus is mucin glycoprotein that enables gel formation. Due to the molecular nature of mucin, it interacts with most substances including polyanionic biopolymers like alginates. Alginate molecules have been extensively used in pharmaceutical and medical industries as mediators because they possess suitable characteristics for a variety of biomedical applications. They have also been shown to influence mucus rheology, and could hold potential to alter other properties of mucus as well, such as particle mobility. In this thesis, the effect of different molecular weight alginates were investigated on the rheology of porcine gastric (PG) mucin, porcine small intestinal mucus (PSIM), porcine tracheobronchial mucus (PTBM) and bio-similar mucus. In addition, the effect of alginate on particle mobility in PG mucin samples were investigated using multiple particle tracking (MPT). The rheological effect of alginate G-block DPn 12, DPn 24, DPn 33 and alginate LFR 5/60 on PG mucin was inconclusive as the sample suffered from pH and mechanical instabilities. Particle mobility was greatest for G-block DPn 12 and G-block DPn 33 treated PG mucin at long time scales. In addition, their mean-square displacement (MSD) trajectories were more narrowly distributed than the other samples, which correlates to a higher degree of uniform pore sizes. The rheological behaviour of bio-similar mucus and PSIM after treatment of G-block DPn 12, G-block DPn 33 and LFR 5/60 did not coincide, despite bio-similar mucus being a model system for porcine intestinal mucus (PIM). This was ascribed interactions between alginate and polyacrylate in the bio-similar mucus causing phase separation. Alginate G-block DPn 12 weakened the PSIM and PTBM gel, while G-block DPn 33 and LFR 5/60 had minor strengthening effects on PSIM.
Effects of humic substances isolated from earthworm faeces.

Earthworm biomass and activity in soil are highly related to the nature of vegetable organic wastes and are controlled by climatic conditions, food composition, physical and chemical soil characteristics. Earthworms strongly affect soil fertility by increasing the availability of nutrients, improving soil structure and water-holding capacity, but the main effect of earthworms in soil concerns the control of the humification process. It has been suggested that earthworms can increase the velocity of organic residue decomposition and also produce faeces rich in bioactive humus. While the role played by earthworms in the growth and productivity of plants was previously related to their effects on soil structure, recent work has suggested that these effects may be due to the production of faeces that contain more than 40% of humic substances endowed with hormone-like activity. This mini-review summarizes the progress made in recent years on the effects of humic substances isolated from earthworm faeces. Some specific issues will focus on the effects of earthworms on humification processes, plant growth and physiological processes in plant tissues. _____________________________________________________________________________________________________________
Influence of increased level of methionine in diets on disappearance rate of amino acids (AA) from yolk sac protein and ileal digestibility of AA in chickens and ducks.

Two experiments were carried out on Hubbard HI-Ye broiler chickens and A11 Pekin ducks. On day 1, exactly 5 h after hatch, 30 chickens and 30 ducks were selected and then killed in order to determine the chemical composition of yolk sac residues. Other birds in both experiments were assigned into 5 treatments (every with 6 or 4 replications) and fed mixtures containing gradually increased levels of methionine (crystalline DL-Met 99 %) 0.30 (control), 0.33; 0.37; 0.42 and 0.48 %. The purpose of these studies was to determine the effect of increased dietary methionine on yolk sac (YS) absorption rate as estimated on day 1 st , 3 rd , 5 th ,7 th
Effect of Vitiligo Area Scoring Index on the quality of life in patients with vitiligo

Objective The aim of this study was to find out the relation between the vitiligo severity and quality of life of patients with vitiligo. Background Vitiligo is the chronic pigmentary disorder of the skin. It greatly affects psychological well-being, and patients experience poor body image and low self-esteem, which may lead to lower level of life quality. Patients and methods Overall, 203 patients with vitiligo were studied. Disease severity was assessed using Vitiligo Area Scoring Index (VASI), and patients were asked to answer the Dermatology Life Quality Index (DLQI) questionnaire. DLQI scores and subscores were calculated, and disease characteristics were evaluated. Results Mean age of all patients was 26.21 years. The overall DLQI mean score was 5.80 ± 5.04. The DLQI mean score was 6.68 and 3.16 in women and men, respectively. In 18.2% of patients with vitiligo, no effect was seen on the DLQI, little effect was reported in 35% of patients, moderate effect was seen in 32.5% of patients, and extremely high effect was seen in 3% of them. VASI, duration of diseases, and site of lesion were significantly positively correlated with DLQI score. Conclusion VASI, duration of the disease, and site of the lesion were positively correlated with DLQI score. Concentrating on patient's life quality is essential in the management of patients with vitiligo. Moreover, significantly strong gathering-based consultations and treatments are additionally imperative arms for dealing with vitiligo.
Variability among Alternaria solani isolates causing early blight of tomato

Variability among isolates of Alternaria solani, the causal agent of early blight of tomato, from Northern and Southern parts of India was determined based on conidial morphology, pathogenicity tests and random amplified polymorphic DNA (RAPD) technique. The isolates varied with respect to size of conidia and number of septa. The test isolates differed in the virulence pattern on ten tomato genotypes under screen house conditions. Isolates RAS (Rohtak) and HAS- I (Hisar) were more virulent than all other isolates. The analysis of RAPD profiles showed that there was a high level of genetic variability among the isolates of A. solani. The cluster analysis based on similarity coefficients separated the ten A. solani isolates into two major clusters. There was no evidence for geographical clustering of isolates with high levels of genetic similarity, suggesting that isolates are widely spread across India.
Prokaryotic cell wall compounds : structure and biochemistry

Cell Wall Polymers and Structures of Bacteria. - The Murein Sacculus. - Occurrence, Structure, Chemistry, Genetics, Morphogenesis, and Functions of S-Layers. - Bacterial Polysaccharide Capsules. - Lipopolysaccharides. - Structure, Biosynthesis, and Function of Teichoic Acids and Related Cell Wall Glycopolymers in the Gram-positive Cell Envelope. - Outer Membrane Proteins. - Cell Wall Polymers and Structures of Archaea. - Cell Envelopes of Methanogens. - The Cell Envelopes of Haloarchaea: Staying in Shape in a World of Salt. - Cell Envelopes of Crenarchaeota and Nanoarchaeota. - Biological Activities. - Immunochemistry of the Cell Walls of Methanogenic Archaea: A View from the Past into the Future. - Cell Wall Structure and Pathogenicity. - Cell Wall Growth and Inhibition. - Cell Wall Targeted Antibiotics. - Bacterial Autolysins. - Cell Wall Interactions. - Prokaryotic Cell-Cell Interaction. - Adhesion of Bacteria to Protists. - Application of Cell Wall Components. - Prokaryotic Cell Wall Components: Structure and Biochemistry. - Accumulation of Heavy Metals by Micro-organisms: Biomineralization and Nanocluster Formation.
Signatures of niche conservatism and niche shift in the North American kudzu (Pueraria montana) invasion

Recent advances have improved our ability to determine the degree to which the climatic niche of invasive populations resembles (niche conservatism) or differs from (niche shift) that of native progenitors. We compared the climatic niche of kudzu (Pueraria montana), one of the most devastating invasive species in North America, between its native (East Asia) and invasive (United States) ranges.
Influence of β-carotene and vitamin A supplementation on the ovarian activity of dairy cows with chronic fertility impairment.

TROJAČANEC, S. , S. BOBOŠ, M. PAJIĆ: Infl uence of β-carotene and vitamin A supplementation on the ovarian activity of dairy cows with chronic fertility impairment. Vet. arhiv 82, 567-575, 2012. ABSTRACT The aim of this study was to determine the infl uence of supplemented β-carotene and vitamin A on the ovarian activity during the periovulatory period in dairy cows with chronic fertility impairment. A total of 46 non pregnant Holstein cows with fertility impairment, at the age of 5-7 years, were selected for this study. The animals in three experimental groups were supplemented wit h either a combination of β-carotene and vitamin A, β-carotene only or vitamin A only. Non supplemented animals served as controls. All animals included in the survey were gynecologically examined; the estrus was synchronized and inseminated. Initial blood levels of β-carotene as well as the levels at the time of insemination and in the luteal phase as well as the ovarian structures during ovulation and formation of corpus luteum and P4 and conception rate, were monitored. Signifi cant increases in follicular size as well as luteal tissue growth were found in animals supplemented with β-carotene and vitamin A combination and vitamin A only. Positive correlation between the serum concentrations of β-carotene at insemination and at day 7 of the luteal phase and the concentrations of progesterone and the conception rate, lead to a conclusion that periovulatory β-carotene and and vitamin A supplementation could improve follicular growth and development of the corpora lutea in cows with fertility impairement.
The Role of SmpB in Licensing tmRNA Entry into Stalled Ribosomes

The Role of SmpB in Licensing tmRNA Entry into Stalled Ribosomes Mickey R. Miller Department of Chemistry and Biochemistry, BYU Doctor of Philosophy Ribosomes translate the genetic information contained in mRNAs into protein by linking together amino acids with the help of aminoacyl-tRNAs. In bacteria, protein synthesis stalls when the ribosome reaches the 3’-end of truncated mRNA transcripts lacking a stop codon. Trans-translation is a conserved bacterial quality control process that rescues stalled ribosomes. Transfer-messenger RNA (tmRNA) and its protein partner SmpB mimic a tRNA by entering the A site of the ribosome and accepting the growing peptide chain. The ribosome releases the truncated mRNA and resumes translation on the tmRNA template. The open reading frame found on tmRNA encodes a peptide tag that marks the defective nascent peptide for proteolysis. A stop codon at the end of the open reading frame allows the ribosome to be recycled and engage in future rounds of translation. The entry of tmRNA into stalled ribosomes presents a challenge to our understanding of ribosome function because during the canonical decoding process, the ribosome specifically recognizes the codon-anticodon duplex formed between tRNA and mRNA in the A site. Recognition of proper base-pairing leads to conformational changes that accelerate GTP hydrolysis by EF-Tu and rapid accommodation of the tRNA into the ribosome for peptidyl transfer. The puzzle is that tmRNA enters stalled ribosomes and reacts with the nascent peptide in the absence of a codon-anticodon interaction. Instead, SmpB binding in the decoding center begins the rescue process, but it has been unclear how SmpB licenses tmRNA entry into stalled ribosomes. We analyzed a series of SmpB and ribosomal RNA mutants using pre-steady-state kinetic assays for EF-Tu activation and peptidyl transfer. Although the conserved 16S nucleotides A1492 and A1493 play an essential role in canonical decoding, they play little or no role in EF-Tu activation or peptidyl transfer to tmRNA. In contrast, a third nucleotide, G530, stacks with the side chain of SmpB residue His136, inducing conformational changes that lead to GTP hydrolysis by EF-Tu. A portion of the C-terminal tail forms a helix within the mRNA channel, monitoring the length of mRNA bound in the ribosome to avoid aborting productive protein synthesis. Helix formation in the mRNA channel is essential for accommodation and peptidyl transfer, but not for GTP hydrolysis. We show that conserved residues in the tail are essential for EFTu activation, accommodation, or translocation to the P site. Our findings lead to a clearer model of how the tmRNA-SmpB complex enters stalled ribosomes.