Fast splice site detection using information content and feature reduction

Background: Accurate identification of splice sites in DNA sequences plays a key role in the prediction of gene structure in eukaryotes. Already many computational methods have been proposed for the detection of splice sites and some of them showed high prediction accuracy. However, most of these methods are limited in terms of their long computation time when applied to whole genome sequence data. Results: In this paper we propose a hybrid algorithm which combines several effective and informative input features with the state of the art support vector machine (SVM). To obtain the input features we employ information content method based on Shannon\u27s information theory, Shapiro\u27s score scheme, and Markovian probabilities. We also use a feature elimination scheme to reduce the less informative features from the input data. Conclusion: In this study we propose a new feature based splice site detection method that shows improved acceptor and donor splice site detection in DNA sequences when the performance is compared with various state of the art and well known method

Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress

BACKGROUND: In our previous studies, we found that the sites in prokaryotic genomes which are most susceptible to duplex destabilization under the negative superhelical stresses that occur in vivo are statistically highly significantly associated with intergenic regions that are known or inferred to contain promoters. In this report we investigate how this structural property, either alone or together with other structural and sequence attributes, may be used to search prokaryotic genomes for promoters. RESULTS: We show that the propensity for stress-induced DNA duplex destabilization (SIDD) is closely associated with specific promoter regions. The extent of destabilization in promoter-containing regions is found to be bimodally distributed. When compared with DNA curvature, deformability, thermostability or sequence motif scores within the -10 region, SIDD is found to be the most informative DNA property regarding promoter locations in the E. coli K12 genome. SIDD properties alone perform better at detecting promoter regions than other programs trained on this genome. Because this approach has a very low false positive rate, it can be used to predict with high confidence the subset of promoters that are strongly destabilized. When SIDD properties are combined with -10 motif scores in a linear classification function, they predict promoter regions with better than 80% accuracy. When these methods were tested with promoter and non-promoter sequences from Bacillus subtilis, they achieved similar or higher accuracies. We also present a strictly SIDD-based predictor for annotating promoter sequences in complete microbial genomes. CONCLUSION: In this report we show that the propensity to undergo stress-induced duplex destabilization (SIDD) is a distinctive structural attribute of many prokaryotic promoter sequences. We have developed methods to identify promoter sequences in prokaryotic genomes that use SIDD either as a sole predictor or in combination with other DNA structural and sequence properties. Although these methods cannot predict all the promoter-containing regions in a genome, they do find large sets of potential regions that have high probabilities of being true positives. This approach could be especially valuable for annotating those genomes about which there is limited experimental data

Means to an End: An Assessment of the Status-blind Approach to Protecting Undocumented Worker Rights

This article applies the tenets of bureaucratic incorporation theory to an investigation of bureaucratic decision making in labor standards enforcement agencies (LSEAs), as they relate to undocumented workers. Drawing on 25 semistructured interviews with high-level officials in San Jose and Houston, I find that bureaucrats in both cities routinely evade the issue of immigration status during the claims-making process, and directly challenge employers’ attempts to use the undocumented status of their workers to deflect liability. Respondents offer three institutionalized narratives for this approach: (1) to deter employer demand for undocumented labor, (2) the conviction that the protection of undocumented workers is essential to the agency’s ability to regulate industry standards for all workers, and (3) to clearly demarcate the agency’s jurisdictional boundaries to preserve institutional autonomy and scarce resources. Within this context, enforcing the rights of undocumented workers becomes simply an institutional means to an end

The Greenland and Antarctic ice sheets under 1.5◦C global warming

Even if anthropogenic warming were constrained to less than 2°C above pre-industrial, the Greenland and Antarctic ice sheets will continue to lose mass this century, with rates similar to those observed over the last decade. However, nonlinear responses cannot be excluded, which may lead to larger rates of mass loss. Furthermore, large uncertainties in future projections still remain, pertaining to knowledge gaps in atmospheric (Greenland) and oceanic (Antarctica) forcing. On millennial timescales, both ice sheets have tipping points at or slightly above the 1.5-2.0°C threshold; for Greenland, this may lead to irreversible mass loss due to the surface mass balance elevation feedback, while for Antarctica, this could result in a collapse of major drainage basins due to ice-shelf weakening

Improved annotation of the insect vector of citrus greening disease: Biocuration by a diverse genomics community

The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models.Peer reviewedBiochemistry and Molecular BiologyEntomology and Plant Patholog

Contributing factors to complications and surgical success in mouse kidney transplantation

PURPOSE: Mouse kidney transplantation is a challenging technique for novice microsurgeons. Factors that affect transplant outcomes for a clinical surgeon starting microsurgery have not yet been investigated. MATERIALS AND METHODS: 110 consecutive mouse kidney transplants were performed over a 9-month period. Data were recorded, and surgical results and complication were analyzed. RESULTS: Three and thirty day survival rates improved from 0 (0/6) to 92.3% (12/13) between months 1 and 9. Bleeding, arterial thrombosis, kidney failure and hydronephrosis were the most common causes of transplant failure. From month 1 to month 7, using the same surgical technique, practice significantly decreased the incidence of bleeding and increased the 3-day survival rate; however, it didn't significantly decrease the incidence of thrombosis, kidney failure, but improved the 30-day survival rate. From month 8, when surgical technique used on artery anastomosis switched from continuous suture to interrupted suture, surgical survival rate at 3 and 30 days improved significantly. Interestingly, ischemia time was not a significant factor determining the success of transplantation in this study. CONCLUSIONS: Practice is essential for novice microsurgeons, and the choice of surgical techniques significantly affects surgical results. The use of interrupted arterial sutures can significantly improve mouse kidney transplantation outcomes compared with continuous sutures. Ischemic time was not a factor in determining successful of kidney transplantation in mice in this study

Epithelial-mesenchymal interactions in prostatic development. I. morphological observations of prostatic induction by urogenital sinus mesenchyme in epithelium of the adult rodent urinary bladder.

Tissue recombinants of embryonic urogenital sinus mesenchyme (UGM) and epithelium of the urinary bladder (urothelium, BLE) of adult rats and mice were grown for 3-30 d in male syngeneic hosts. Short-term in vivo growth indicated that prostatic morphogenesis is initiated as focal outgrowths from the basal aspect of the adult urothelium. The solid epithelial buds elongate, branch, and subsequently canalize, forming prostatic acini. After 30 d of growth in the male hosts, prostatic acini exhibit secretory activity. The marked changes in urothelial morphology induced by the UGM are accompanied by the expression of fine-structural features indicative of secretory function (rough endoplasmic reticulum, Golgi apparatus, and secretory granules). During this process, urothelial cells express prostatic histochemical markers (alkaline phosphatase, nonspecific esterase, glycosaminoglycans) and prostate-specific antigens. The expression within BLE of prostatic characteristics is associated with the loss of urothelial characteristics. These data indicate that adult urothelial cells retain a responsiveness to embryonic mesenchymal inductors. Furthermore, mesenchyme-induced changes in urothelial cytodifferentiation appear to be coupled to changes in functional activity