Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional and structural analysis of MOZART1, an essential MTOC regulator

-Tubulin plays a universal role in microtubule nucleation from microtubule organizing centers (MTOCs), such as the centrosome in higher eukaryotes and the spindle pole body (SPB) in fungi. The -Tubulin functions as part of a multiprotein complex called the -tubulin Ring complex (-TuRC), consisting of -tubulin complex protein (GCP) 1–6, where GCP1 is tubulin. It has been shown that GCP1–3 are core components as they are essential and are absolutely required for the -TuRC assembly, whereas the other three GCPs are not. Recently, a novel component of the -TuRC, MOZART1, has been identified in humans and plants. In humans, MOZART1 plays an essential role in mitotic spindle formation as a component of the -TuRC. The precise functional role of MOZART1 is still yet unknown. In this thesis, I therefore aimed to reveal its mode of action at a molecular level. For this purpose, I chose to exploit a powerful model system, fission yeast, which allows us to take multidisciplinary approaches. The mzt1 (also known as tam4) gene, which encodes fission yeast MOZART1 homologue, is essential. I localised Mzt1 during mitosis and meiosis and found it at the MTOCs. It also coimmunoprecipitates with -tubulin from cell extracts. I also determined the starting methionine of the mzt1 gene which encodes a 64–amino acid peptide. Depletion of Mzt1 leads to aberrant microtubule structure, including malformed mitotic spindles and impaired interphase microtubule array. It also causes cytokinesis defects, suggesting a role of the -tubulin complex (-TuC) in the regulation of cytokinesis. Yeast two-hybrid analysis shows that Mzt1 interacts with GCP3, a fission yeast homologue of GCP3. Biophysical methods demonstrate that there is a direct interaction between recombinant Mzt1 and the N-terminal region of GCP3. In addition Mzt1 protein tends to oligomerize into trimer or hexamer. Collectively I propose that Mzt1 oligomer directly interacts with GCP3 and stabilizes the -TuC to facilitate microtubule regulation.
Fragile X related protein-1 (FXR1) regulates RNA metabolism in striated muscle

Cardiac muscle function necessitates the meticulous assembly and inter act ons of several cytoskeletal and regulatory proteins into specialized structure s that orchestrate contraction and transmission forces. Despite extensive studies identifying the pro ein components responsible for these important aspects of heart development, putative RNA based mechanisms remain poorly understood, even with their demonstrated importance in other tissues. Evidence suggests that post-transcriptional regulation is crit ical for muscle function, but the molecular players involved (RNA binding proteins and mRNA targets) have remained elusive. We investigated the molecular mechanisms and targets of th muscle-specific Fragile X Related protein-1 (FXR1), an RNA binding pro tein whose absence leads to perinatal lethality in mice. Loss of FXR1 results in globa l pr tein level alterations. Morphological and biochemical analyses of Fxr1 mice revealed severe disruption of intercalated disc and costamere architecture and composition. We identified several candidate mRNAs specifically enriched in the FXR1 protein complex . Two targets that likely contribute to the architectural defects are desmoplakin (dsp) and talin2 (tln2). In vitro assays indicate that FXR1 binds to these mRNA targets directly and represses their translation. Additionally, we provide preliminary evidence t hat the Fxr1 mice mimic a hypothyroid state of cardiac gene expression, with alterations in myosin heavy chain and troponin I isoforms. Our findings reveal the first mRNA tar gets of FXR1 in muscle and support translational repression as a novel mechanism for cardia c muscle development and function.
Cognitive apprenticeship in clinical practice; Can it be extended to postgraduate psychiatry training programmes?

Introduction: Postgraduate psychiatry training occurs in the workplace or situated learning settings. The Cognitive Apprenticeship Model [CAM] was introduced as an instructional model for situated learning. While undergraduate medical students' experience of the model has been tested, to our knowledge there has been no such reports from postgraduate psychiatry training. Methods: We surveyed 134 Oxford Deanery psychiatry trainees recruited between 2005 and 2013 through an online questionnaire. Respondents identified which CAM components [scaffolding, modelling coaching, articulation, reflection exploration] were the best aspects, and most needing improvement, in their clinical training. Results: Of 57 respondents, 80% were satisfied with and enjoyed [90%] their training. They recognised all individual CAM components; modelling and coaching were identified as the best methods. Exploration was identified as the one most in need of improvement. The behavioural [modelling, coaching and scaffolding] rather than the cognitive methods were identified as the best aspects of their training [54 v 35%, p < 0.001]. Conclusions: The results extend findings from undergraduate students in suggesting that the CAM is a useful model for training strategies. Greater awareness of the cognitive components may be needed. The training methods could be included as indicators of training quality in national quality assurance surveys.
Physiological effects of climate on distributions of endothermic species

Aim Determining the mechanisms underlying climatic limitation of species distributions is essential for understanding responses to current climatic change. Disentangling direct (e.g. physiological) and indirect (e.g. trophic) effects of climate on distributions through occurrence‐based modelling is problematic because most species use the same area for both shelter and food acquisition. By focusing on marine birds that breed on land but feed at sea, we exploit a rare opportunity to dissociate direct from indirect climatic effects on endothermic species.
Evolutionary genomics of symbiotic fungi

Ectomycorrhizae is a mutualistic association between roots of woody plants and a diverse range of soil fungi. The fungi exchange soil derived mineral nutrients for photosynthetic sugars from the host plant. The mycorrhizal symbioses are commonly found in all forest ecosystems and have a major ecological and economical importance. I have used comparative genomics, DNA microarrays and computational approaches to gain insights into the evolution of the ectomycorrhizal symbiosis in two fungi Laccaria bicolor (Basidiomycetes; Agaricales) and Paxillus involutus (Basidiomycetes; Boletales). L. bicolor is the first symbiotic fungus to have its genome sequence determined. The genome assembly contains 65 million base pairs with about ~20,000 predicted protein-encoding genes. Here, I report the analysis of L. bicolor genome and its comparison with the genomes of four other basidiomycetes including the saprotrophic species Coprinopsis cinerea and Phanerochaete chrysosporium, the human pathogen Cryptococcus neoformans and the plant pathogen Ustilago maydis. The compared genomes cover about 550 million years of evolution. A total of 58,030 protein sequences from these five basidiomycetes were clustered into 7352 protein families. The evolution of protein families were analysed for accelerated rates of gain and loss along specific branches of a phylogenetic tree using a stochastic birth and death model. Analysis of the genome sequence of L. bicolor in comparison to other analysed basidiomycetes revealed large genome size, large number of protein families, larger size of protein families, many lineage specific and expanded families, and large number of recent duplicates. The evolution of two large and expanded protein families in L. bicolor having significant homology to protein kinases and Ras GTPases superfamilies were analysed in more detail. The analyses showed these families to contain many paralogs that have arisen through recent duplication events. The comparative analyses of gene families showed that the evolution of symbiosis in L. bicolor has been associated with the expansion of large multigene families. The functions of many of these families are unknown but many of them are differentially expressed during symbiosis. In the second part of my thesis, I have analysed duplicated and rapidly evolving genes that could be associated with symbiotic adaptations in the ectomycorrhizal fungus P. involutus. Strains of P. involutus forming ectomycorrhiza showing various degree of host-specificity were analysed by comparative genomic hybridizations using a cDNA microarray representing 1076 putative unique genes. Approximately 17% of the genes investigated on the array were detected as rapidly and presumably non-neutrally evolving within Paxillus. Among these genes, there were several hydrophobins. Hydrophobins are small, secreted hydrophobic cell surface proteins having several roles in growth and development of fungi. The evolutionary mechanisms responsible for generating sequence and expression divergence among members of the hydrophobin multigene family in P. involutus were examined in more detail. (Less)
Outbreaks of Bemisia tabaci in Sao Paulo State.

Since 1991, an increase in the populations of the whitefly Bemisia tabaci (Genn.) (Homoptera: Aleyrodidae) infesting vegetables and ornamental plants in some localities of Sao Paulo State, Brazil, has been observed. High densities of this insect were verified on tomato, broccoli, egg-plant and squash; in some cases, tomato and squash presented the whitefly-related disorders named tomato irregular repening and squash silverleaf. Weeds, mainly Sida rhombifolia L. , Sonchus oleraceus L. , Solanum viarum Dun. and Ipomoea acuminata Roem. & Schult. , showed high whitefly colonization. At the Holambra county intensive colonizations were recorded on or-namental plants, mainly Chrysanthemum morifolium Ramat. and Euphorbia pulcherrima Willd. (poinsettia). Daily insecticide applications did not reduce the insect infestations. Other crops, such as bean and cotton, were also infested. The disorders and type of infestations are similar to what has been observed in the U.S.A. In this country, the ability of certain populations of B. tabaci to induce the silverleaf disorder of squash and to colonize poinsettia intensely, among other characteristics, has been used to distinguish the "poinsettia strain" or "B strain". However, based on genomic and crossing/mating behavior studies, some investigators have considered that these two strains represent different species. In view of the similarity of the infestations and disorders that are occurring in the U.S.A. , and more recently in Sao Paulo State, it is very likely that the "B strain" (or the new species) has been introduced in Brazil.
An integrative exploratory analysis of –omics data from the ICGC cancer genomes lung adenocarcinoma study

It is known that all agents that cause cancer (carcinogens) also cause a change in the DNA sequence. In order to identify such often subtle changes, we attempt to integrate multiple molecular profile data sets released by the International Cancer Genome Consortium (ICGC). The list of data sets includes matched gene and microRNA expression profiles, somatic copy number variation, DNA methylation, and protein expression profiles for lung adenocarcinoma patients receiving treatments. We consider both unsupervised and supervised learning techniques (clustering and penalized regression) to identify interesting molecular markers corresponding to each type of –omics profiles that can differentiate patients. Associations between important markers of 2 types have been studied. An adaptive ensemble binary regression model has been presented that uses the entirety of available –omics profiles leading to a more accurate clinical prognosis for the patients in the given sample. This integrated study provides a more comprehensive picture of lung adenocarcinoma.
Perceptions of public sector practitioners about records and information management surveys in zimbabwe

This article aims at establishing public sector records practitioners‟ perceptions about records and information management surveys which are periodically held by the National Archives of Zimbabwe (NAZ). The urge to carry out the study emanated from the continuing poor records management practices in public sector departments in Zimbabwe despite the fact that NAZ carries out periodic records and information management surveys. This study was carried out in the City of Gweru in Zimbabwe and it employed a survey research design where data were collected using questionnaires and interviews. The study revealed that public records practitioners largely had negative perceptions about NAZ records surveys as they saw the exercise as intrusive and faultfinding. NAZ officers blamed the impasse on lack of knowledge about the importance of records and lack of professional training in records management. The study recommends that NAZ officers should be sleuth and diplomatic when conducting records surveys to promote good relations and as well, there is need for behavior change on the part of public records practitioners for them to develop positive perceptions about NAZ records and information management surveys.
COMPARATIVE STUDY ON HYDROLYTIC ENZYMES PRODUCED BY DIFFERENT MORPHOLOGICAL FORMS OF CANDIDA ALBICANS

In recent years, the incidence of fungal infections has been rising all over the world. The ability of Candida albicans to switch from yeast to hyphal growth is essential for its virulence. The aim of this comparative study was to biotype and characterize phospholipase, proteinase, phosphatase and haemolytic activities of yeast and hyphal forms of Candida albicans . The hyphal form of Candida albicans secrets high quantity of hydrolytic enzymes than yeast form, which helps in its virulence. These results suggest that pathogenic fungi produce larger amount of inducible hydrolytic enzymes than non-pathogenic fungi. In this investigation, plate methods were used to determine the phospholipase, proteinase and haemolytic activities and spectrophotometric method was employed for testing acid phosphatase activity. Keywords: Candida albicans , Candidiasis, Hydrolytic enzymes, Haemolytic activity, Virulence.
Protein profi le and serodiagnosis of Taenia solium bladder worm infections in pigs

A study on the protein profi le of the bladder worms of Taenia solium was conducted. Three antigens, including whole cyst antigen (WCA), scolex antigen (SA) and excretory secretory antigen (ESA), were evaluated and the presence of 18, 15 and 12 polypeptides was observed, respectively. The WCA, SA and ESA had 11, 10 and 9 polypeptides respectively as immunodominant when these were allowed to react with homologous hyper immune sera. When infected pig sera were allowed to react, 4 bands in WCA, 2 in SA and 4 in ESA were found to be highly reactive.
Gene Complexes and their role in Worker Honeybee (Apis mellifera) Ovary Activation

iii Honeybees (Apis mellifera) are remarkable creatures with a complex eusocial hive structure. There are two female honeybee castes within a hive; a single queen and thousands of workers. The only reproductively active female is the queen. However, should the hive lose its queen (removing the pheromone she produces, queen mandibular pheromone, which keeps the workers in a reproductively inactive state), the ovaries of worker honeybees differentiate from the quiescent state they are normally in and begin to produce eggs. This remarkable remodelling of adult tissue in response to a changing environment occurs rapidly (within ten days) and is accompanied by changes in the expression of thousands of genes. It was hypothesised that this rapid response may be facilitated by the genome being organised into functional domains, known as gene complexes, containing a number of neighbouring genes which were all upregulated or repressed together to produce the rapid morphological and functional changes observed within the worker honeybee ovary. This study began by investigating whether one of the three known honeybee gene complexes was involved in worker ovary activation. The Enhancer of Split Complex [E(Spl)-C] is expressed in response to Notch signalling and as Notch signalling plays a role in Drosophila oogenesis this complex was chosen for investigation by RT-qPCR. This study found that the canonical E(Spl)-C genes were regulated in the same manner as each other during worker ovary activation, although the Tubulin-Tyrosine Kinase-like gene which is inserted within the canonical E(Spl)-C and which is co-ordinately regulated with these genes in development), is expressed in an opposite manner to the rest of this genomic region during worker ovary activation. The identification of a CCCTC-binding factor (CTCF) binding site within this region implies that changes in the three dimensional structure of the DNA may be responsible for the Tubulin-Tyrosine Kinase evading the co-ordinate gene regulation in this region. To test whether there were other, previously uncharacterised, gene complexes involved in worker ovary activation an RNA-Seq data set which compared the expression of all known honeybee genes between queen ovary, quiescent worker ovary and active worker ovary was analysed using the existing programme REEF (REgionally Enriched Features of genomes). When REEF was found to be limited in its approach, a new programme was written (using the C++ programming language) to identify novel gene complexes expressed within the honeybee ovary. Overall, there was less evidence of association
Digital economy and green development: Empirical evidence from China’s cities

With prominent environmental pollution and depleted resources, how to coordinate economic growth and eco-environmental protection to guide green development represented by green total factor productivity (GTFP) is an urgent issue. This study aims to empirically evaluate the direct effect, indirect effect, spatial spillover effect and non-linear effect of the digital economy on green development using the data of 284 prefecture-level cities in China. The empirical results indicate that: (1) the digital economy significantly improves GTFP, which is still valid after testing for robustness, including introducing instrumental variables, taking the “broadband China” pilot policy as a quasi-natural experiment, changing core explanatory variables and dependent variables, and changing the sample size; (2) the influence of the digital economy on GTFP is characterized by significant heterogeneity among resource dependence, geographical location, financial development level and openness level; (3) the mechanism analysis shows that the digital economy promotes GTFP by green technological innovation, industrial structure upgrading and energy conservation; (4) the spatial econometric models indicate that the digital economy significantly enhances GTFP of neighboring cities; (5) there is a non-linear relationship between the digital economy and GTFP using the threshold model. The findings could provide references for policymakers to promote urban green development.
Efeito da cianamida hidrogenada na quebra de dormência das gemas, produtividade do vinhedo e composição química do mosto da uva Cabernet Sauvignon

A pulverizacao de cianamida hidrogenada em varas de videira, Vitis vinifera L. cv. Cabernet Sauvignon, por ocasiao da poda seca, nas concentracoes de 0, 1, 3 e 5%, teve um efeito significativo sobre as variaveis percentagem de gemas brotadas numero de cachos por planta, fertilidade por gema e produtividade por gema e do vinhedo. A analise de regressao polinomial mostra que houve um efeito quadratico significativo, e que os pontos de maximo para estas variaveis foram obtidos com concentracoes entre 1,8% e 1,9%. Entretanto, ela nao teve efeito significativo sobre peso por cacho, peso por baga e produtividade por gema brotada, nem sobre o Brix, acidez total, Brix/acidez total, pH, densidade, P, K, Ca e Mg do mosto da uva. Quando comparada com a testemunha, a aplicacao de cianamida hidrogenada a 1% antecipou a brotacao em quatro dias; na concentracao de 5%, retardou-a em 18 dias. Ela tambem uniformizou a brotacao e diminuiu ou suprimiu a dominância apical.
What you Know is What you Parse : How situational knowledge affects sentence processing

You will never believe what happened at the party yesterday! Ellen kissed Ruben and Peter…. Suppose this is the last thing you read in your friend’s e-mail before your computer breaks down. If you have some prior knowledge regarding the situation described, you would be able to guess how the interrupted sentence could continue without great difficulty. For example, if you know that Ellen was secretly in love with both Peter and Ruben and you know she has a certain reputation, she may have kissed them both, but if you know she has a crush on Ruben, but definitely not on Peter, the remaining part of the sentence would more likely be something like (Ellen kissed Ruben and Peter) smiled his approval from a distance. The main question of the research presented in this dissertation is whether readers’ knowledge of a situation immediately affects the structural analysis (i.e. parse) of a sentence. This knowledge is called situational knowledge and is provided by means of discourse context. More generally, the question is whether non-syntactic factors immediately affect the initial parse of a sentence or whether it is solely determined on the basis of syntax-based parsing preferences. Syntactic ambiguity, specifically, the NP-/S-coordination ambiguity, is used as a research tool. The aim is to demonstrate effects of situational knowledge not only at the point of disambiguation, but also at the onset of the ambiguity. A second question is how situational knowledge interacts with other, particularly syntactic factors. In order to investigate this question, the influence of situational knowledge is not only investigated in isolation, but also in contrast to another factor, viz. subject-verb agreement. In particular, it is investigated which factor outweighs the other if both factors conflict. Results of a series of off-line experiments, self-paced reading experiments and an eye movement experiment are discussed. The results show that the parsing process is immediately affected by situational knowledge, a non-syntactic factor that is often even considered non-linguistic. Furthermore, it turns out that a syntactic constraint (in this case subject-verb agreement) eventually overrules the initial analysis of the critical sentence as determined by situational knowledge. On the basis of these results, parsing is argued to be a highly interactive, dynamic process that changes in response to the strength of various sources of information. This dissertation should be of interest to those interested in sentence processing and its interfaces with discourse representation.
Number of individuals and molecular markers to use in genetic differentiation studies

Molecular markers are frequently used to study genetic variation among individuals within or between populations. Differences in marker banding patterns can be used to verify if individuals do, or do not, represent distinct groups or populations. Only in 2005, more than 500 studies used molecular markers to group individuals in clusters. Such studies make use of an arbitrary number of molecular markers from each of an arbitrary number of individuals presumed to represent distinct genotypes. However, the greater the genetic variation, the more likely a larger number of individuals and markers will be needed to capture a population's genetic signature. The numbers of both, markers and individuals included thus affect the way in which individuals are organized through cluster analyses, thereby affecting the conclusions drawn. Here we present a method that provides statistical criteria to verify that individual and marker sample sizes are sufficient to accurately depict genetic differentiation among different populations. Our method uses a resampling technique to assess the reproducibility of obtaining a particular grouping pattern for specific data sets. It thus, allows to estimate the robustness of the results obtained without including additional individuals, or markers.