The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

BACKGROUND: Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, well-organized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields. RESULTS: We have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (1) Current Comparative Structure Models; (2) Nucleotide Frequency and Conservation Information; (3) Sequence and Structure Data; and (4) Data Access Systems. CONCLUSIONS: This online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW) Site http://www.rna.icmb.utexas.edu. In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site

BRCAness Profile of Sporadic Ovarian Cancer Predicts Disease Recurrence

BACKGROUND:The consequences of defective homologous recombination (HR) are not understood in sporadic ovarian cancer, nor have the potential role of HR proteins other than BRCA1 and BRCA2 been clearly defined. However, it is clear that defects in HR and other DNA repair pathways are important to the effectiveness of current therapies. We hypothesize that a subset of sporadic ovarian carcinomas may harbor anomalies in HR pathways, and that a BRCAness profile (defects in HR or other DNA repair pathways) could influence response rate and survival after treatment with platinum drugs. Clinical availability of a BRCAness profile in patients and/or tumors should improve treatment outcomes. OBJECTIVE:To define the BRCAness profile of sporadic ovarian carcinoma and determine whether BRCA1, PARP, FANCD2, PTEN, H2AX, ATM, and P53 protein expression correlates with response to treatment, disease recurrence, and recurrence-free survival. MATERIALS AND METHODS:Protein microarray analysis of ovarian cancer tissue was used to determine protein expression levels for defined DNA repair proteins. Correlation with clinical and pathologic parameters in 186 patients with advanced stage III-IV and grade 3 ovarian cancer was analyzed using Chi square, Kaplan-Meier method, Cox proportional hazard model, and cumulative incidence function. RESULTS:High PARP, FANCD2 and BRCA1 expressions were significantly correlated with each other; however, elevated p53 expression was associated only with high PARP and FANCD2. Of all patients, 9% recurred within the first year. Among early recurring patients, 41% had high levels of PARP, FANCD2 and P53, compared to 19.5% of patients without early recurrence (p = 0.04). Women with high levels of PARP, FANCD2 and/or P53 had first year cumulative cancer incidence of 17% compared with 7% for the other groups (P = 0.03). CONCLUSIONS:Patients with concomitantly high levels of PARP, FANCD2 and P53 protein expression are at increased risk of early ovarian cancer recurrence and platinum resistance

EDUCATIONAL DATA MINING IN THE FIELD OF HIGHER EDUCATION-A SURVEY

As we know that in today the higher education is important for every human being. The new trends and techniques are playing very crucial and important role to improve the quality of higher education. Now we need some more sophisticated and emerging trends that turns to improve the quality of higher education. Educational Data Mining is one of the emerging trends that concerned with developing methods for exploring the unique types of data that come from educational settings, and using those methods to better understand students, and the settings which they learn in

Rhesus Cytomegalovirus Contains Functional Homologues of US2, US3, US6, and US11

Human cytomegalovirus (HCMV) is a paradigm for mechanisms subverting antigen presentation by major histocompatibility complex (MHC) molecules. Due to its limited host range, HCMV cannot be studied in animals. Thus, the in vivo importance of inhibiting antigen presentation for the establishment and maintenance of infection with HCMV is unknown. Rhesus cytomegalovirus (RhCMV) is an emerging animal model that shares many of the features of HCMV infection. The recent completion of the genomic sequence of RhCMV revealed a significant degree of homology to HCMV. Strikingly, RhCMV contains several genes with low homology to the HCMV US6 gene family of inhibitors of the MHC I antigen presentation pathway. Here, we examine whether the RhCMV US6 homologues (open reading frames Rh182, -184, -185, -186, -187, and -189) interfere with the MHC I antigen-processing pathway. We demonstrate that Rh182 and Rh189 function similarly to HCMV US2 and US11, respectively, mediating the proteasomal degradation of newly synthesized MHC I. The US3 homologue, Rh184, delayed MHC I maturation. Unlike US3, MHC I molecules eventually escaped retention by Rh184, so that steady-state surface levels of MHC I remained unchanged. Rh185 acted similarly to US6 and inhibited peptide transport by TAP and, consequently, peptide loading of MHC I molecules. Thus, despite relatively low sequence conservation, US6 family-related genes in RhCMV are functionally closely related to the conserved structural features of HCMV immunomodulators. The conservation of these mechanisms implies their importance for immune evasion in vivo, a question that can now be addressed experimentally

LxCxD motif of the APC/C coactivator subunit FZR1 is critical for interaction with the retinoblastoma protein

10.1016/j.yexcr.2021.112632EXPERIMENTAL CELL RESEARCH404

An evaluation of patient's decisions regarding dental prosthetic treatment

Introduction: For fabricating dental prostheses that meet patients' demands and have good longevity and function, appropriate treatment planning and decision-making are required. Therefore, not only technical skills and clinical judgment of the dentist are needed, but also patients' attitude toward treatment plays a critical role in posttreatment satisfaction. Aim: The aim of this study is to investigate the factors affecting decision-making and the selection of dental prosthesis by the patients. Materials and Methods: A cross-sectional survey to determine patients' attitudes about replacement of teeth was conducted. This survey was performed with the help of a prevalidated questionnaire, which contained the demographic data of every patient, whether or not they accept the treatment plan proposed by the dentist, and a close-ended multiple choice question stating the reasons cited by them if they decline the proposed treatment plan. Results: The data were subjected to statistical analysis by Chi-square test at a significance level of P< 0.05. A relationship between the demographical information such as age, gender, educational status, marital status, and monthly income of each patient and the single best reason opted by them to not undergo the proposed treatment plan was established. Conclusions: In the sample of population studied, most of the patients declined the proposed treatment plan and accepted the alternate one. High expenditure is the most common reason for this rejection

The Associations of P53, BRCAness Profile and Residual Tumor with 3-year Recurrence-Free Survival.

<p>*Negative is defined as no or weak staining; positive is defined as moderate or strong staining.</p

Association between Early Recurrence and Positive P53, PARP, and FANCD2.

<p>Association between positive P53, PARP, and FANCD2 in patients with and without early recurrence. Patients with early recurrence at both 6 and 12 months after diagnosis were much more likely to have high levels of all 3 proteins (50% at 6 months and 41.2% at 12 months).</p

Kaplan-Meier Estimated 3-Year Recurrence-Free Survival Curves.

<p>Kaplan-Meier estimated 3-year recurrence-free survival curves. <b>A:</b> No difference in recurrence-free survival when each of the 5 mutually exclusive groups by expression of PARP, FANCD2, and P53 were examined independently. <b>B:</b> Patients positive for all three PARP, FANCD2, and P53 had lower recurrence-free survival compared to patients not positive for all three.</p