Mapping Post-translational Modifications of Mammalian Testicular Specific Histone Variant TH2B in Tetraploid and Haploid Germ Cells and Their Implications on the Dynamics of Nucleosome Structure

Histones regulate a variety of chromatin templated events by their post-translational modifications (PTMs). Although there are extensive reports on the PTMs of canonical histones, the information on the histone variants remains very scanty. Here, we report the identification of different PTMs, such as acetylation, methylation, and phosphorylation of a major mammalian histone variant TH2B. Our mass spectrometric analysis has led to the identification of both conserved and unique modifications across tetraploid spermatocytes and haploid spermatids. We have also computationally derived the 3-dimensional model of a TH2B containing nucleosome in order to study the spatial orientation of the PTMs identified and their effect on nucleosome stability and DNA binding potential. From our nucleosome model, it is evident that substititution of specific amino acid residues in TH2B results in both differential histone-DNA and histone-histone contacts. Furthermore, we have also observed that acetylation on the N-terminal tail of TH2B weakens the interactions with the DNA. These results provide direct evidence that, similar to somatic H2B, the testis specific histone TH2B also undergoes multiple PTMs, suggesting the possibility of chromatin regulation by such covalent modifications in mammalian male germ cells.

Reversible induction of translational isoforms of p53 in glucose deprivation

Tumor suppressor protein p53 is a master transcription regulator, indispensable for controlling several cellular pathways. Earlier work in our laboratory led to the identification of dual internal ribosome entry site (IRES) structure of p53 mRNA that regulates translation of full-length p53 and Delta 40p53. IRES-mediated translation of both isoforms is enhanced under different stress conditions that induce DNA damage, ionizing radiation and endoplasmic reticulum stress, oncogene-induced senescence and cancer. In this study, we addressed nutrient-mediated translational regulation of p53 mRNA using glucose depletion. In cell lines, this nutrient-depletion stress relatively induced p53 IRES activities from bicistronic reporter constructs with concomitant increase in levels of p53 isoforms. Surprisingly, we found scaffold/matrix attachment region-binding protein 1 (SMAR1), a predominantly nuclear protein is abundant in the cytoplasm under glucose deprivation. Importantly under these conditions polypyrimidine-tract-binding protein, an established p53 ITAF did not show nuclear-cytoplasmic relocalization highlighting the novelty of SMAR1-mediated control in stress. In vivo studies in mice revealed starvation-induced increase in SMAR1, p53 and Delta 40p53 levels that was reversible on dietary replenishment. SMAR1 associated with p53 IRES sequences ex vivo, with an increase in interaction on glucose starvation. RNAi-mediated-transient SMAR1 knockdown decreased p53 IRES activities in normal conditions and under glucose deprivation, this being reflected in changes in mRNAs in the p53 and Delta 40p53 target genes involved in cell-cycle arrest, metabolism and apoptosis such as p21, TIGAR and Bax. This study provides a new physiological insight into the regulation of this critical tumor suppressor in nutrient starvation, also suggesting important functions of the p53 isoforms in these conditions as evident from the downstream transcriptional target activation.

Translation Induction on Indian Language Corpora Using Translingual Themes from Other Languages

Identifying translations from comparable corpora is a well-known problem with several applications, e.g. dictionary creation in resource-scarce languages. Scarcity of high quality corpora, especially in Indian languages, makes this problem hard, e.g. state-of-the-art techniques achieve a mean reciprocal rank (MRR) of 0.66 for English-Italian, and a mere 0.187 for Telugu-Kannada. There exist comparable corpora in many Indian languages with other ``auxiliary'' languages. We observe that translations have many topically related words in common in the auxiliary language. To model this, we define the notion of a translingual theme, a set of topically related words from auxiliary language corpora, and present a probabilistic framework for translation induction. Extensive experiments on 35 comparable corpora using English and French as auxiliary languages show that this approach can yield dramatic improvements in performance (e.g. MRR improves by 124% to 0.419 for Telugu-Kannada). A user study on WikiTSu, a system for cross-lingual Wikipedia title suggestion that uses our approach, shows a 20% improvement in the quality of titles suggested.

Effects of Translational Nonequilibrium on Performance of Flowing Chemical Oxygen-Iodine Laser

The effect of the translational nonequilibrium on performance modeling of flowing chemical oxygen-iodine lasers (COIL) is emphasized in this paper. The spectral line broadening (SLB) model is a basic factor for predicting the performances of flowing COIL. The Voigt profile function is a well-known SLB model and is usually utilized. In the case of gas pressure in laser cavity less than 5 torr, a low pressure limit expression of the Voigt profile function is used. These two SLB models imply that ail lasing particles can interact with monochromatic laser radiation. Basically, the inhomogeneous broadening effects are not considered in these two SLB models and they cannot predict the spectral content. The latter requires consideration of finite translational relaxation rate. Unfortunately, it is rather difficult to solve simultaneously the Navier-Stokes (NS) equations and the conservation equations of the number of lasing particles per unit volume and per unit frequency interval. In the operating condition of flowing COIL, it is possible to obtain a perturbational solution of the conservational equations for lasing particles and deduce a new relation between the gain and the optical intensity, i.e., a new gain-saturation relation. By coupling the gain-saturation relation with other governing equations (such as the NS equations, chemical reaction equations and the optical model of gain-equal-loss), We have numerically calculated the performances of flowing COIL. The present results are compared with those obtained by the common rate-equation (RE) model, in which the Voigt profile function and its low pressure limit expression are used. The difference of different model's results is great. For instance, in the case of lasing frequency coinciding with the central frequency of line profile and very low gas pressure, the gain-saturation relation of the present model is quite different with that of the RE model.

"Empty bed blues": Terry McMillan's Waiting to Exhale (1992), novel into film

Santamaría, José Miguel; Pajares, Eterio; Olsen, Vickie; Merino, Raquel; Eguíluz, Federico (eds.)

Bilingual Lexicography:Relevance of Corpora. The Example of German-Basque as Language Pair

Presentation for the 5th International Conference on Corpus Linguistics (CILC 2013), V Congreso Internacional de Lingüistica de Corpus.

Single cell proteomics microchip to profile immune function, with applications in stem cell biology, translational disease mechanism study and clinical therapeutics monitoring

In response to infection or tissue dysfunction, immune cells develop into highly heterogeneous repertoires with diverse functions. Capturing the full spectrum of these functions requires analysis of large numbers of effector molecules from single cells. However, currently only 3-5 functional proteins can be measured from single cells. We developed a single cell functional proteomics approach that integrates a microchip platform with multiplex cell purification. This approach can quantitate 20 proteins from >5,000 phenotypically pure single cells simultaneously. With a 1-million fold miniaturization, the system can detect down to ~100 molecules and requires only ~104 cells. Single cell functional proteomic analysis finds broad applications in basic, translational and clinical studies. In the three studies conducted, it yielded critical insights for understanding clinical cancer immunotherapy, inflammatory bowel disease (IBD) mechanism and hematopoietic stem cell (HSC) biology.

To study phenotypically defined cell populations, single cell barcode microchips were coupled with upstream multiplex cell purification based on up to 11 parameters. Statistical algorithms were developed to process and model the high dimensional readouts. This analysis evaluates rare cells and is versatile for various cells and proteins. (1) We conducted an immune monitoring study of a phase 2 cancer cellular immunotherapy clinical trial that used T-cell receptor (TCR) transgenic T cells as major therapeutics to treat metastatic melanoma. We evaluated the functional proteome of 4 antigen-specific, phenotypically defined T cell populations from peripheral blood of 3 patients across 8 time points. (2) Natural killer (NK) cells can play a protective role in chronic inflammation and their surface receptor – killer immunoglobulin-like receptor (KIR) – has been identified as a risk factor of IBD. We compared the functional behavior of NK cells that had differential KIR expressions. These NK cells were retrieved from the blood of 12 patients with different genetic backgrounds. (3) HSCs are the progenitors of immune cells and are thought to have no immediate functional capacity against pathogen. However, recent studies identified expression of Toll-like receptors (TLRs) on HSCs. We studied the functional capacity of HSCs upon TLR activation. The comparison of HSCs from wild-type mice against those from genetics knock-out mouse models elucidates the responding signaling pathway.

In all three cases, we observed profound functional heterogeneity within phenotypically defined cells. Polyfunctional cells that conduct multiple functions also produce those proteins in large amounts. They dominate the immune response. In the cancer immunotherapy, the strong cytotoxic and antitumor functions from transgenic TCR T cells contributed to a ~30% tumor reduction immediately after the therapy. However, this infused immune response disappeared within 2-3 weeks. Later on, some patients gained a second antitumor response, consisted of the emergence of endogenous antitumor cytotoxic T cells and their production of multiple antitumor functions. These patients showed more effective long-term tumor control. In the IBD mechanism study, we noticed that, compared with others, NK cells expressing KIR2DL3 receptor secreted a large array of effector proteins, such as TNF-α, CCLs and CXCLs. The functions from these cells regulated disease-contributing cells and protected host tissues. Their existence correlated with IBD disease susceptibility. In the HSC study, the HSCs exhibited functional capacity by producing TNF-α, IL-6 and GM-CSF. TLR stimulation activated the NF-κB signaling in HSCs. Single cell functional proteome contains rich information that is independent from the genome and transcriptome. In all three cases, functional proteomic evaluation uncovered critical biological insights that would not be resolved otherwise. The integrated single cell functional proteomic analysis constructed a detail kinetic picture of the immune response that took place during the clinical cancer immunotherapy. It revealed concrete functional evidence that connected genetics to IBD disease susceptibility. Further, it provided predictors that correlated with clinical responses and pathogenic outcomes.

Novel roles of the SRP RNA in co-translational protein targeting

The signal recognition particle (SRP) and its receptor (SR) are universally conserved protein machineries that deliver nascent peptides to their proper destination. The SRP RNA is a universally conserved and essential component of SRP, which serves as the “catalyst” of the protein targeting cycle. The SRP RNA accelerates SRP-SR complex formation at the beginning of the protein targeting reaction, and triggers GTP hydrolysis and SRP-SR complex disassembly at the end. Here we combined biochemical and biophysical approaches to investigate the molecular mechanism of the functions of the SRP RNA. We found that two functional ends in the SRP RNA mediate distinct functions. The tetraloop end facilitates initial assembly of SRP and SR by mediating an electrostatic interaction with the Lys399 receptor, which ensures efficient and accurate substrate targeting. At the later stage of the SRP cycle, the SRP-SR complex relocalizes ~ 100 Angstrom to the 5’,3’-distal end of the RNA, a conformation crucial for GTPase activation and cargo handover. These results, combined with recent structural work, elucidate the functions of the SRP RNA during the protein targeting reaction.

Behavior of spherical particles at low Reynolds numbers in a fluctuating translational flow

The behavior of spheres in non-steady translational flow has been studied experimentally for values of Reynolds number from 0.2 to 3000. The aim of the work was to improve our qualitative understanding of particle transport in turbulent gaseous media, a process of extreme importance in power plants and energy transfer mechanisms.

Particles, subjected to sinusoidal oscillations parallel to the direction of steady translation, were found to have changes in average drag coefficient depending upon their translational Reynolds number, the density ratio, and the dimensionless frequency and amplitude of the oscillations. When the Reynolds number based on sphere diameter was less than 200, the oscillation had negligible effect on the average particle drag.

For Reynolds numbers exceeding 300, the coefficient of the mean drag was increased significantly in a particular frequency range. For example, at a Reynolds number of 3000, a 25 per cent increase in drag coefficient can be produced with an amplitude of oscillation of only 2 per cent of the sphere diameter, providing the frequency is near the frequency at which vortices would be shed in a steady flow at the mean speed. Flow visualization shows that over a wide range of frequencies, the vortex shedding frequency locks in to the oscillation frequency. Maximum effect at the natural frequency and lock-in show that a non-linear interaction between wake vortex shedding and the oscillation is responsible for the increase in drag.

Prosa argumentativa em língua inglesa: um estudo contrastivo sobre advérbios em corpora digitais

Esta pesquisa tem como objetivo principal investigar como aprendizes brasileiros de língua inglesa usam advérbios com terminação em ly no inglês escrito, e comparar ao uso que deles fazem os falantes de inglês como língua materna. Para tanto, o trabalho encontra suporte teórico e metodológico na Linguística de Corpus e fundamenta-se na área chamada de pesquisa sobre corpora de aprendizes, que se ocupa da coleta e armazenagem de dados linguísticos de sujeitos aprendizes de uma língua estrangeira, para a formação de um corpus que possa ser utilizado para fins descritivos e pedagógicos. Esta área objetiva identificar em que aspectos os aprendizes diferem ou se assemelham aos falantes nativos. Os corpora empregados na pesquisa são o corpus de estudo (Br-ICLE), contendo inglês escrito por brasileiros, compilado de acordo com o projeto ICLE (International Corpus of Learner English) e dois corpora de referência (LOCNESS e BAWE), contendo inglês escrito por falantes de inglês como língua materna. Os resultados indicam que os alunos brasileiros usam, em demasia, as categorias de advérbios que indicam veracidade, realidade e intensidade, em relação ao uso que deles fazem os falantes nativos, além de usarem esses advérbios de forma distinta. Os resultados sugerem que, além das diferenças apresentadas em termos de frequência (seja pelo sobreuso ou subuso dos advérbios), os aprendizes apresentavam combinações errôneas, ou em termos de colocados ou em termos de prosódia semântica. E finalmente a pesquisa revela que a preferência dos aprendizes por advérbios que exprimem veracidade, realidade e intensidade cria a impressão de um discurso muito assertivo. Conclui-se que as diferenças encontradas podem estar ligadas a fatores como o tamanho dos corpora, a influência da língua materna dos aprendizes, a internalização dos elementos linguísticos necessários para a produção de um texto em língua estrangeira, a falta de fluência dos aprendizes e o contexto de sala de aula nas universidades

Normas Tradutórias: o caso dos Artigos Científicos e suas Condicionantes Culturais

Esta dissertação investiga o gênero artigo científico e suas condicionantes culturais, ou seja, as marcas textuais que podem apresentar determinada dificuldade para o tradutor por problemas de interculturalidade, a partir da perspectiva do conceito de normas nos estudos da tradução e da descrição do gênero artigo científico. O objetivo deste trabalho é identificar estas condicionantes em artigos científicos da área de Geriatria e Gerontologia, exemplificando partes deste universo de condicionantes através do levantamento das características desse gênero, assim como da comparação das traduções. Demonstrar através da reflexão teórica, de exemplos práticos e de análises comparativas, como a tradução se beneficia do estudo de gêneros, das normas e do levantamento das condicionantes culturais para auxiliar a tarefa tradutória de artigos científicos. Os procedimentos de análise dos corpora foram baseados no modelo de Lambert e Van Gorp (1985) para a análise da tradução literária, adaptado aqui à tradução técnica. Finalmente, analisando as condicionantes culturais levantadas nesta pesquisa, assim como as características do gênero, o estudo culmina com reflexões a respeito da tradução de artigos científicos