Molecular characterization of Arabidopsis thaliana PUF proteins - binding specificity and target candidates

PUF proteins regulate both stability and translation through sequence-specific binding to the 3` UTR of target mRNA transcripts. Binding is mediated by a conserved PUF domain, which contains eight repeats of approximately 36 amino acids each. Found in all eukaryotes, they have been related to several developmental processes. Analysis of the 25 Arabidopsis Pumilio (APUM) proteins presenting PUF repeats reveals that 12 (APUM-1 to APUM-12) have a PUF domain with 50-75% similarity to the Drosophila PUF domain. Through three-hybrid assays, we show that APUM-1 to APUM-6 can bind specifically to the Nanos response element sequence recognized by Drosophila Pumilio. Using an Arabidopsis RNA library in a three-hybrid screening, we were able to identify an APUM-binding consensus sequence. Computational analysis allowed us to identify the APUM-binding element within the 3` UTR in many Arabidopsis transcripts, even in important mRNAs related to shoot stem cell maintenance. We demonstrate that APUM-1 to APUM-6 are able to bind specifically to APUM-binding elements in the 3` UTR of WUSCHEL, CLAVATA-1, PINHEAD/ZWILLE and FASCIATA-2 transcripts. The results obtained in the present study indicate that the APUM proteins may act as regulators in Arabidopsis through an evolutionarily conserved mechanism, which may open up a new approach for investigating mRNA regulation in plants.

Gene expression profiling reveals molecular marker candidates of laryngeal squamous cell carcinoma

Laryngeal squamous cell carcinoma is very common in head and neck cancer, with high mortality rates and poor prognosis. In this study, we compared expression profiles of clinical samples from 13 larynx tumors and 10 non-neoplastic larynx tissues using a custom-built cDNA microarray containing 331 probes for 284 genes previously identified by informatics analysis of EST databases as markers of head and neck tumors. Thirty-five genes showed statistically significant differences (SNR >= 11.01, p <= 0.001) in the expression between tumor and non-tumor larynx tissue samples. Functional annotation indicated that these genes are involved in cellular processes relevant to the cancer phenotype, such as apoptosis, cell cycle, DNA repair, proteolysis, protease inhibition, signal transduction and transcriptional regulation. Six of the identified transcripts map to intronic regions of protein-coding genes and may comprise non-annotated exons or as yet uncharacterized long ncRNAs with a regulatory role in the gene expression program of larynx tissue. The differential expression of 10 of these genes (ADCY6, AES, AL2SCR3, CRR9, CSTB, DUSP1, MAP3K5, PLAT, UBL1 and ZNF706) was independently confirmed by quantitative real-time RT-PCR. Among these, the CSTB gene product has cysteine protease inhibitor activity that has been associated with an antimetastatic function. Interestingly, CSTB showed a low expression in the tumor samples analyzed (p<0.0001). The set of genes identified here contribute to a better understanding of the molecular basis of larynx cancer, and provide candidate markers for improving diagnosis, prognosis and treatment of this carcinoma.

Screening the Schistosoma mansoni transcriptome for genes differentially expressed in the schistosomulum stage in search for vaccine candidates

Schistosomiasis affects more than 200 million people worldwide; another 600 million are at risk of infection. The schistosomulum stage is believed to be the target of protective immunity in the attenuated cercaria vaccine model. In an attempt to identify genes up-regulated in the schistosomulum stage in relation to cercaria, we explored the Schistosoma mansoni transcriptome by looking at the relative frequency of reads in EST libraries from both stages. The 400 genes potentially up-regulated in schistosomula were analyzed as to their Gene Ontology categorization, and we have focused on those encoding-predicted proteins with no similarity to proteins of other organisms, assuming they could be parasite-specific proteins important for survival in the host. Up-regulation in schistosomulum relative to cercaria was validated with real-time reverse transcription polymerase chain reaction (RT-PCR) for five out of nine selected genes (56%). We tested their protective potential in mice through immunization with DNA vaccines followed by a parasite challenge. Worm burden reductions of 16-17% were observed for one of them, indicating its protective potential. Our results demonstrate the value and caveats of using stage-associated frequency of ESTs as an indication of differential expression coupled to DNA vaccine screening in the identification of novel proteins to be further investigated as potential vaccine candidates.

Race as political strategy by US presidential candidates: a case study

Race has played an important part in US presidential politics in contemporary history. Different political parties and candidates have followed covert strategies playing on the prejudices of white voters both cognitively and emotionally by linking racerelated issues to the majority's individual and group interests. This elite discourse carried to the public by the mainstream media, along with media's practices of stereotyping, priming, framing and agenda setting, help to justify racial prejudice, discrimination against minorities and their marginalized status, while maintaining the status quo. Taking the social constructionist position, this case study examines the opinions expressed by a sample of undecided voters selected from different geographic locations at various stages of the 1992 US presidential campaign under the themes 'Candidates' racial prejudice' and 'Race is used as political strategy by candidates.'

Doctoral research and scholarly communication : candidates, supervisors and information literacy

This study investigates information literacy and scholarly communication within the processes of doctoral research and supervision at a distance. Both doctoral candidates and supervisors acknowledge information literacy deficiencies and it is suggested that disintermediation and the proliferation of information may contribute to those deficiencies. Further to this, the influence of pedagogic continuity—particularly in relation to the information seeking behaviour of candidates—is investigated, as is the concomitant aspect of how doctoral researchers practise scholarly communication. The well-documented and enduring problem for candidates of isolation from the research cultures of their universities is also scrutinised. The contentious issue of more formally involving librarians in the doctoral process is also considered, from the perspective of candidates and supervisors. Superimposed upon these topical and timely issues is the theoretical framework of adult learning theory, in particular the tenets of andragogy. The pedagogical-andragogical orientation of candidates and supervisors is established, demonstrating both the differences and similarities between candidates and supervisors, as are a number of independent variables, including a comparison of on-campus and off-campus candidates. Other independent variables include age, gender, DETYA (Department of Education, Training & Youth Affairs) category, enrolment type, stage of candidature, employment and status, type of doctorate, and English/non-English speaking background. The research methodology uses qualitative and quantitative techniques encompassing both data and methodological triangulation. The study uses two sets of questionnaires and a series of in-depth interviews with a sample of on-campus and off-campus doctoral candidates and supervisors from four Australian universities. Major findings include NESB candidates being more pedagogical than their ESB counterparts, and candidates and supervisors from the Sciences are more pedagogical than those from Arts, Humanities and Social Sciences, or Education. Candidates make a transition from a more dependent and pedagogically oriented approach to learning towards more of an independent and andragogical orientation over the duration of their candidature. However, over tune both on-campus and off-campus candidates become more isolated from the research cultures of their universities, and less happy with support received from their supervisors in relation to their literature reviews. Ill The study found large discrepancies in perception between the support supervisors believed they gave to candidates in relation to the literature review, and the support candidates believed they received. Information seeking becomes easier over time, but candidates face a dilemma with the proliferation of information, suggesting that disintermediation has exacerbated the challenges of evaluation and organisation of information. The concept of pedagogic continuity was recognised by supervisors and especially candidates, both negative and positive influences. The findings are critically analysed and synthesised using the metaphor of a scholarly 'Club' of which obtaining a doctorate is a rite of passage. Recommendations are made for changes in professional practice, and topics that may warrant further research are suggested.

How shall we know them? Capturing the diversity of difference in Australian doctoral candidates and their experiences.

Although there is general agreement that doctoral students and their experiences are diverse, in what respect this is true is in question. Most institutional practices in the collection of data in this regard have been established to satisfy government reporting requirements and concerns, such as funding, participation and equity, and efficiency. Missing is more detailed and nuanced quantitative data and analysis, complementary to those of qualitative studies, to illuminate the nature and extent of doctoral student diversity and the effects on the quality of their candidacy. Drawing on select data and findings from a national survey of Australian doctoral candidates conducted in 2005, the article questions the utility of commonly used categories for quantitative data collection and analysis, and their use as the basis of (sub)groupings to represent doctoral diversity. In so doing, it presents a more complex picture of doctoral candidature that depicts the idiosyncrasy of the individual experience, as well as generic characteristics. Central to the argument is that doctoral candidates are diversely different, bringing varying goals, expectations, career histories and family and community responsibilities beyond the academy, that shape their engagement with their candidacy.

Characterization of mucus-associated proteins from abalone (Haliotis) – candidates for chemical signaling

Living in groups is a widespread phenomenon in the animal kingdom. For free-spawning aquatic animals, such as the abalone (Haliotis), being in the close proximity to potential mating partners enhances reproductive success. In this study, we investigated whether chemical cues could be present in abalone mucus that enable species-specific aggregation. A comparative MS analysis of mucus obtained from trailing or fixed stationary Haliotis asinina, and from seawater surrounding aggregations, indicated that water-soluble biomolecules are present and that these can stimulate sensory activity in conspecifics. Purified extracts of trail mucus contain at least three small proteins [termed H. asinina mucus-associated proteins (Has-MAPs)-1–3], which readily diffuse into the surrounding seawater and evoke a robust cephalic tentacle response in conspecifics. Mature Has-MAP-1 is approximately 9.9 kDa in size, and has a glycine-rich N-terminal region. Has-MAP-2 is approximately 6.2 kDa in size, and has similarities to schistosomin, a protein that is known to play a role in mollusc reproduction. The mature Has-MAP-3 is approximately 12.5 kDa in size, and could only be identified within trail mucus of animals outside of the reproductive season. All three Has-MAP genes are expressed at high levels within secretory cells of the juvenile abalone posterior pedal gland, consistent with a role in scent marking. We infer from these results that abalone mucus-associated proteins are candidate chemical cues that could provide informational cues to conspecifics living in close proximity and, given their apparent stability and hydrophilicity, animals further afield.

Efflux pumps of Mycobacterium tuberculosis play a significant role in antituberculosis activity of potential drug candidates

Active efflux of drugs mediated by efflux pumps that confer drug resistance is one of the mechanisms developed by bacteria to counter the adverse effects of antibiotics and chemicals. To understand these efflux mechanisms in Mycobacterium tuberculosis, we generated knockout (KO) mutants of four efflux pumps of the pathogen belonging to different classes. We measured the MICs and kill values of two different compound classes on the wild type (WT) and the efflux pump (EP) KO mutants in the presence and absence of the efflux inhibitors verapamil and L-phenylalanyl-L-arginyl-β-naphthylamide (PAβN). Among the pumps studied, the efflux pumps belonging to the ABC (ATP-binding cassette) class, encoded by Rv1218c, and the SMR (small multidrug resistance) class, encoded by Rv3065, appear to play important roles in mediating the efflux of different chemical classes and antibiotics. Efflux pumps encoded by Rv0849 and Rv1258c also mediate the efflux of these compounds, but to a lesser extent. Increased killing is observed in WT M. tuberculosis cells by these compounds in the presence of either verapamil or PAβN. The efflux pump KO mutants were more susceptible to these compounds in the presence of efflux inhibitors. We have shown that these four efflux pumps of M. tuberculosis play a vital role in mediating efflux of different chemical scaffolds. Inhibitors of one or several of these efflux pumps could have a significant impact in the treatment of tuberculosis. The identification and characterization of Rv0849, a new efflux pump belonging to the MFS (major facilitator superfamily) class, are reported.

Validity of the Beck Depression Inventory as a screening tool for a clinical mood disorder in Bariatric surgery candidates

Background : The Beck Depression Inventory (BDI) is one of the most commonly used instruments to assess depression in persons with obesity. While it has been validated in normal and psychiatric populations, in obese populations, its validity remains uncertain. This study aimed to investigate the validity and reliability of the BDI-IA and BDI-II in severely obese bariatric surgery candidates.

Methods : Consecutive new candidates at a bariatric surgery clinic were invited to participate in the study by their consulting surgeon. All candidates were assessed using the Structured Clinical Interview for DSM-IV Disorders (SCID-I); 118 completed the BDI-IA and 83 completed the BDI-II. Two hundred one patients (response rate, 88 %) participated in the study. The current sample (82 % female) had an average body mass index of 42.83 ± 6.34 and an average age of 45 ± 12 years.

Results : Based on the SCID-I, 54 candidates (26.9 %) met the criteria for a mood disorder, with 37 meeting the criteria for current major depressive disorder. Individuals diagnosed with a clinical mood disorder had significantly higher scores on the BDI (BDI-IA, 23.59 ± 9.69 vs. 12.76 ± 8.29; BDI-II, 22.93 ± 5.22 vs. 11.25 ± 8.44). Our results indicated that, as a screening tool for a clinical mood disorder, the BDI-II had an optimal cutoff of 13, with a sensitivity of 100 and specificity of 67.75.

Conclusions : Results indicated that the BDI-IA should not be used as a tool to measure depressive symptomatology in obese bariatric surgery candidates. No cutoff was identified with adequate sensitivity and specificity, and over 20 % of patients were misclassified. As a screening tool for a clinical mood disorder, the BDI-II was adequate; however, prevalence rates were significantly overestimated.

A view to lead India : who are the candidates?

 India will go to the polls from April 5 to May 12 to choose between three party leaders for its next prime minister. The first is a seasoned politician and three-time chief minister, the Bharatiya Janata Party’s (BJP, or Indian People’s Party) Narendra Modi. The second is a youth icon without experience in governance, Indian National Congress’ Rahul Gandhi. Finally, there is a former bureaucrat and utopian visionary who resigned from the post of chief minister, Arvind Kejriwal.