Optimization of in vitro multiplication for exotic banana (Musa spp.) in Pakistan

The present attempt aimed to optimize micropropagation protocols supplemented with different concentrations and combinations of benzylaminopurine (BAP) (0, 2, 4, 6 mg L-1) and indole acetic acid (IAA) (0.5 and 1.0 mg L-1). Exotic banana (Musa spp) genotypes GCTCV-215 (AAA), ‘Yangambi’ Yangambi Km-5 (AAA) and FHIA-23 (AAAA) were used in research work. Experiments were conducted at Plant Tissue Culture Laboratory of Nuclear Institute of Agriculture (NIA), Tando Jam. Data collected for in vitro shoot consists of the following parameters: days for bud initiation, rate of shoot proliferation (%), number of multiple shoots, shoot length (cm) and fresh mass of shoot (g). Significant (p≤ 0.05) variations were observed for varieties, treatments and varieties x treatment for all the parameters. Synergistic effects of BAP and IAA were observed in GCTCV-215 and Yangambi Km-5. Out of various treatments, best concentration for multiple shoot in short period of time for GCTCV-215 and Yangambi Km-5 was found in 4.0 mg /l BAP + 0.5 mg L-1 IAA. Maximum fresh mass of shoot observed at same concentration and combination of BAP and IAA and for shoot length combination of 4.0 mg L-1 BAP with 1.0 mg L-1 IAA was found to be most suitable for GCTCV-215 and Yangambi Km-5. FHIA-23, show better performance in MS medium supplemented with only BAP at concentration 4.0 mg/L-1. After development of root, in vitro plantlets were shifted from growth room to green house in polythene bags containing garden soil and humus mixture in ratio (1:1).Keywords: Micropropagation efficiency, exotic musa genotype, growth regulators

RNA secondary structure prediction from multi-aligned sequences

It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted. I systematically review and classify existing tools and algorithms for the problem, by utilizing the information employed in the tools and by adopting a unified viewpoint based on maximum expected gain (MEG) estimators. I believe that this classification will allow a deeper understanding of each tool and provide users with useful information for selecting tools for common secondary structure predictions.Comment: A preprint of an invited review manuscript that will be published in a chapter of the book `Methods in Molecular Biology'. Note that this version of the manuscript may differ from the published versio

Nanostructured AgBr loaded TiO2: An efficient sunlight active photocatalyst for degradation of Reactive Red 120

The AgBr loaded TiO2 catalyst was prepared by a feasible approach with AgBr and tetraisopropyl orthotitanate and characterized by BET surface area measurement, diffuse reflectance spectra (DRS), scanning electron microscope (SEM), energy dispersive spectra (EDS), X-ray diffraction (XRD), transmission electron microscope (TEM) and atomic force microscope (AFM) analysis. The results of characterization reveal that AgBr loaded TiO2 has a nanostructure. Formation of the nanostructure in AgBr loaded TiO2 results in substantial shifting of the absorption edge of TiO2 to red and enhancement of visible light absorption. Electrochemical impedance spectroscopy measurements reveal that AgBr loaded TiO2 has a higher photoconductivity than prepared TiO2 due to higher separation efficiency of electron-hole pairs. Cyclic voltammetric studies reveal enhanced conductivity in AgBr loaded TiO2, which causes an increase in its photocatalytic activity. AgBr loaded TiO2 exhibited a higher photocatalytic activity than TiO2-P25 and prepared TiO2 in the photodegradation of Reactive Red 120 (RR 120)

Breast cancer risk factor knowledge among nurses in teaching hospitals of Karachi, Pakistan: a cross-sectional study

BACKGROUND: Breast cancer is the most common cancer among women in both the developed and the developing world. The incidence of breast cancer in Karachi, Pakistan is 69.1 per 100,000 with breast cancer presentation in stages III and IV being common (≥ 50%). The most pragmatic solution to early detection lies in breast cancer education of women. Nurses constitute a special group having characteristics most suited for disseminating breast cancer information to the women. We assessed the level of knowledge of breast cancer risk factors among registered female nurses in teaching hospitals of Karachi. We also identified whether selected factors among nurses were associated with their knowledge of breast cancer risk factors, so that relevant measures to improve knowledge of nurses could be implemented. METHODS: A cross-sectional survey was conducted in seven teaching hospitals of Karachi using stratified random sampling with proportional allocation. A total of 609 registered female nurses were interviewed using a structured questionnaire adapted from the Stager's Comprehensive Breast Cancer Knowledge Test. Knowledge of breast cancer risk factors was categorized into good, fair and poor categories. Ordinal regression was used to identify factors associated with risk knowledge among nurses. RESULTS: Thirty five percent of nurses had good knowledge of risk factors. Graduates from private nursing schools (aOR = 4.23, 95% CI: 2.93, 6.10), nurses who had cared for breast cancer patients (aOR = 1.41, 95% CI: 1.00, 1.99), those having received a breast examination themselves (aOR = 1.56, 95% CI: 1.08, 2.26) or those who ever examined a patient's breast (aOR = 1.87, 95% CI: 1.34, 2.61) were more likely to have good knowledge. CONCLUSION: A relatively small proportion of the nursing population had good level of knowledge of the breast cancer risk factors. This knowledge is associated with nursing school status, professional breast cancer exposure and self history of clinical breast examination. Since only about one-third of the nurses had good knowledge about risk factors, there is a need to introduce breast cancer education in nursing schools particularly in the public sector. Continuing nursing education at the workplace can be of additional benefit

Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice.

Small non-coding RNAs (sncRNAs) are potential vectors at the interface between genes and environment. We found that traumatic stress in early life altered mouse microRNA (miRNA) expression, and behavioral and metabolic responses in the progeny. Injection of sperm RNAs from traumatized males into fertilized wild-type oocytes reproduced the behavioral and metabolic alterations in the resulting offspring.We thank M. Rassoulzadegan and V. Grandjean for help with the sperm purification, F. Manuella and H. Hörster for assistance with the MSUS paradigm, H. Welzl for help with behavior, G. Vernaz for help with western blotting, R. Tweedie-Cullen and P. Nanni for help with mass spectrometry, A. Patrignani for advice on DNA and RNA quality assessment, and A. Chen and A. Brunner for constructive discussions. This work was supported by the Austrian Academy of Sciences, the University of Zürich, the Swiss Federal Institute of Technology, Roche, the Swiss National Science Foundation, and The National Center of Competence in Research “Neural Plasticity and Repair”. P.S. was supported by a Gonville and Caius College fellowship.This is the accepted manuscript. The final version is available in Nature Neuroscience 17, 667–669 (2014), doi:10.1038/nn.369

Expression of Conjoined Genes: Another Mechanism for Gene Regulation in Eukaryotes

From the ENCODE project, it is realized that almost every base of the entire human genome is transcribed. One class of transcripts resulting from this arises from the conjoined gene, which is formed by combining the exons of two or more distinct (parent) genes lying on the same strand of a chromosome. Only a very limited number of such genes are known, and the definition and terminologies used for them are highly variable in the public databases. In this work, we have computationally identified and manually curated 751 conjoined genes (CGs) in the human genome that are supported by at least one mRNA or EST sequence available in the NCBI database. 353 representative CGs, of which 291 (82%) could be confirmed, were subjected to experimental validation using RT-PCR and sequencing methods. We speculate that these genes are arising out of novel functional requirements and are not merely artifacts of transcription, since more than 70% of them are conserved in other vertebrate genomes. The unique splicing patterns exhibited by CGs reveal their possible roles in protein evolution or gene regulation. Novel CGs, for which no transcript is available, could be identified in 80% of randomly selected potential CG forming regions, indicating that their formation is a routine process. Formation of CGs is not only limited to human, as we have also identified 270 CGs in mouse and 227 in drosophila using our approach. Additionally, we propose a novel mechanism for the formation of CGs. Finally, we developed a database, ConjoinG, which contains detailed information about all the CGs (800 in total) identified in the human genome. In summary, our findings reveal new insights about the functionality of CGs in terms of another possible mechanism for gene regulation and genomic evolution and the mechanism leading to their formation

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √ s = 8 TeV with the ATLAS detector

Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb−1 of √ s = 8 TeV data collected in 2012 with the ATLAS detector at the LHC. Events are required to have at least one jet with pT > 120 GeV and no leptons. Nine signal regions are considered with increasing missing transverse momentum requirements between Emiss T > 150 GeV and Emiss T > 700 GeV. Good agreement is observed between the number of events in data and Standard Model expectations. The results are translated into exclusion limits on models with either large extra spatial dimensions, pair production of weakly interacting dark matter candidates, or production of very light gravitinos in a gauge-mediated supersymmetric model. In addition, limits on the production of an invisibly decaying Higgs-like boson leading to similar topologies in the final state are presente