Handling class imbalance problem in miRNA dataset associated with cancer

MiRNAs are small (~22nt long) non-coding RNA sequences; binds to the complementarity target sites in 3'' Untranslated Region (UTR) of mRNA sequences but not restricted to other mRNA regions viz., 5'' UTR and Coding sequences (CDS). Complementarity binding of miRNA to mRNA target sites either results in complete degradation of the mRNA itself or it may regulate the mRNA as an oncogene or as a tumor suppressor gene. However, the exact mechanism involved in identifying a miRNA to be associated with cancer is still unclear. Further, with the outburst in the number of miRNAs sequences recorded every year in miRBase, the gap is still widening mainly due to the laborious and economically unfavorable experimental procedures associated with the functional annotation. Motivated by the fact, we constructed a two-step support vector machine-based predictive model - miRSEQ and miRINT. However, the major pitfall during the construction of the model is the class imbalance problem. Hence, in order to overcome class imbalance problem, in the present study we empirically compare the effectiveness of two different methods viz., Synthetic Minority Oversampling Technique (SMOTE) and cost-senstive learning method. Performance measures were evaluated in terms of Precision and Recall. Based on our result, it was observed that for miRNA dataset with high class imbalance utilized for predicting association of cancer, cost-sensitive method outperformed the oversampling method.     

How can the functional reponse best be determined?

Summary We evaluated three methods for the analysis of functional response data by asking whether a given method could discriminate among functional responses and whether it could accurately identify regions of positive density-dependent predation. We evaluated comparative curve fitting with foraging models, linear least-squares analysis using the angular transformation, and logit analysis. Using data from nature and simulations, we found that the analyses of predation rates with the angular transformation and logit analysis were best at consistently determining the true functional response, i.e. the model used to generate simulated data. These methods also produced the most accurate estimates of the true regions of density dependence. Of these two methods, functional response data best fulfill the assumptions of logit analysis. Angularly transformed predation rates only approximate the assumptions of linear leastsquares analysis for predation rates between 0.1 and 0.9. Lack-of-fit statistics can reveal inadequate fit of a model to a data set where simple regression statistics might erroneously suggest a good match.     

Binding characteristics of dermorphin, and [dermorphin1-7]-beta c-endorphin in rat brain membranes

Dermorphin and a camel beta-endorphin (beta c-EP) analog in which residues 1-7 correspond to the dermorphin sequence ([Dermorphin1-7]-beta c-EP) have been investigated with respect to their receptor binding characteristics using human and camel beta-EP as reference peptides. Tritiated dihydromorphine, [D-Ala2, D-Leu5]-enkephalin, ethylketocyclazocine and human beta-endorphin were used as primary ligands in the rat brain membrane preparation for radioreceptor assay. Camel beta-endorphin was the most potent peptide in all experiments. [Dermorphin1-7]-beta c-EP is significantly less potent towards 3H-ethylketocyclazocine and 3H-[D-Ala2, D-Leu5]-enkephalin but is as potent towards 3H-dihydromorphine and 3H-human beta-endorphin. Dermorphin itself weakly displaces tritiated dihydromorphine, [D-Ala2, D-Leu5]-enkephalin and ethylketocyclazocine (potency relative to camel beta-EP, 1-4%) but it is more potent (9%) in competition with tritiated human beta-endorphin. Dermorphin and the [Dermorphin-1-7]-beta c-EP appear to interact preferentially with mu opiate receptors.     

细胞分裂素生物合成基因在调节一组烟草病理相关蛋白基因表达中的作用

对一组病理相关蛋白基因在烟草 ( N icotiana tabacum cv. Wisconsin 38)中的表达情况进行了研究 ,包括 :碱性几丁质酶、β- 1 ,3-葡萄糖苷酶、渗透蛋白及伸展蛋白。RNA杂交实验表明在正常烟草植株中上述 4个基因具有发育和器官专一性的表达。在含有细胞分裂素生物合成基因的转基因烟草丛生芽中 ,这 4个基因的表达受过量合成的内源细胞分裂素和载体效应的共同调节 ,细胞分裂素降低这些基因的表达 ,而载体效应则促进它们的表达。热激处理也明显降低这 4种基因的表达水平。上述结果表明这些病理相关蛋白基因具有复杂的调控系统     

小鼠卵母细胞减数分裂染色体的制备

PreparationofMeioticKarytypeofMouseOocyteLiChaojunYanLeipingZhangXiranChenYifeng(BiologyDepartmentofNanjingNormalUniversity,Nanjing210097)哺乳动物的卵母细胞的减数分裂过程中存在两次自发的停滞现象,第一次是在第一次减数分裂前期的双线期,这一静止期持续很长时间,一直到动物性成熟后卵母细胞进入发有周刎,在保住腺激素的作用下,卵母细胞的第一次减数分裂才重新启动．完成第一次减数分裂后．又停滞在第二次减数分裂的中期,在椅子或化学因素刺激的作用下,完成第二次减数分裂[4]．因此,对哺乳动物的卵母细胞在一…     

A three-phase pattern in growth, monoclonal antibody production, and metabolite exchange in a hybridoma bioreactor culture

The use of partial cubic spline data interpolation for the calculation of volumetric metabolite exchange rates suggested the existence of three distinct metabolic phases during bioreactor culture of a hybridoma cell line. During phase 1, a rapid amino acid uptake rate and ammonia release rate were observed. The growth rate was low and glutamine synthetase activity fell. In phase 2, maximum growth rate and minimum glutamine assimilation and ammonium production rates were observed. Attempts to corroborate the apparent ammonia assimilation in this phase using (15)NH(4)Cl resulted in low incorporation rates into alanine and glutamine. Maximum glutamine synthetase activity took place during this period. Maximum antibody production rate was observed during phase 3 during which peaks in glutamine assimilation, ammonia release, and glutamine synthetase activity were observed. The apparent existence of the three phases prompted us to carry out Northern blot analysis of glutamine synthetase RNA at appropriate times during the process. This revealed a pattern of appearance and dis-appearance of mRNA consistent with the three phases indicated by the fermentation parameters. (c) 1993 John Wiley & Sons, Inc.     

Unseen fungal biodiversity and complex inter-organismal interactions in Protea flower heads

A unique microbiome occurs within the flower heads of various Protea species endemic to Africa. These include two lineages of ophiostomatoid fungi, Knoxdaviesia (Microascales) and Sporothrix (Ophiostomatales), that have members occurring exclusively in this environment and that rely on mites as their primary mode of spore dissemination. The mites, in turn, attach to the bodies of Protea-pollinating beetles and the beaks and bodies of birds for long-distance movement, establishing a hierarchical dispersal network for the ophiostomatoid fungi. This inter-organismal network is highly successful, achieving fungal dispersal over vast distances. Multiple species of fungi, mites and bacteria have been described from this unique niche over the past four decades. The intricacies of their symbiotic interactions continue to be unravelled. This review covers all current knowledge of the “distinctly African” Protea-ophiostomatoid fungus environment and illustrates the depth of a fascinating unseen fungal biodiversity niche.     

Local helix content in an alanine-rich peptide as determined by the complete set of 3JHNα coupling constants

Summary Alanine-rich peptides serve as models for exploring the factors that control helix structure in peptides and proteins. Scalar CH-NH couplings (³J_HN) are an extremely useful measure of local helix content; however, the large alanine content in these peptides leads to significant signal overlap in the CH region of ¹H 2D NMR spectra. Quantitative determination of all possible ³J_HN values is, therefore, very challenging. Szyperski and co-workers [(1992) J. Magn. Reson., 99, 552–560] have recently developed a method for determining ³J_HN from NOESY spectra. Because ³J_HN may be determined from 2D peaks outside of the CH region, there is a much greater likelihood of identifying resolved resonances and measuring the associated coupling constants. It is demonstrated here that ³J_HN can be obtained for every residue in the helical peptide Ac-(AAAAK)₃A-NH₂. The resulting ³J_HN profile clearly identifies a helical structure in the middle of the peptide and further suggests that the respective helix termini unfold via distinct pathways.Abbreviations ³J_HN three-bond CH-NH scalar coupling constant - NOE nuclear Overhauser enhancement - NOESY two-dimensional nuclear Overhauser spectroscopy - COSY two-dimensional correlated spectroscopy - DQF-COSY two-dimensional double-quantum-filtered correlated spectroscopy - TOCSY two-dimensional total correlation spectroscopy To whom correspondence should be addressed.Deceased March 5, 1996.