HMM sampling and applications to gene finding and alternative splicing

The standard method of applying hidden Markov models to biological problems is to find a Viterbi (maximal weight) path through the HMM graph. The Viterbi algorithm reduces the problem of finding the most likely hidden state sequence that explains given observations, to a dynamic programming problem for corresponding directed acyclic graphs. For example, in the gene finding application, the HMM is used to find the most likely underlying gene structure given a DNA sequence. In this note we discuss the applications of sampling methods for HMMs. The standard sampling algorithm for HMMs is a variant of the common forward-backward and backtrack algorithms, and has already been applied in the context of Gibbs sampling methods. Nevetheless, the practice of sampling state paths from HMMs does not seem to have been widely adopted, and important applications have been overlooked. We show how sampling can be used for finding alternative splicings for genes, including alternative splicings that are conserved between genes from related organisms. We also show how sampling from the posterior distribution is a natural way to compute probabilities for predicted exons and gene structures being correct under the assumed model. Finally, we describe a new memory efficient sampling algorithm for certain classes of HMMs which provides a practical sampling alternative to the Hirschberg algorithm for optimal alignment. The ideas presented have applications not only to gene finding and HMMs but more generally to stochastic context free grammars and RNA structure prediction.     

Fluorescent cargo proteins in pancreatic beta-cells: design determines secretion kinetics at exocytosis

We compared secretion kinetics for four different fluorescent cargo proteins, each targeted to the lumen of insulin secretory vesicles. Upon stimulation, individual vesicles displayed one of four distinct patterns of fluorescence change: i), disappearance, ii), dimming, iii), transient brightening, or iv), persistent brightening. For each fusion protein, a different pattern of fluorescence change dominated. Furthermore, we demonstrated that the dominant pattern depends upon both i), the specific choice of fluorescent protein, and ii), the sequence of amino acids linking the cargo protein to the fluorescent protein. Thus, in beta-cells, experiments involving fluorescent cargo proteins for the study of exocytosis must be interpreted carefully, as design of a fluorescent cargo protein determines secretion kinetics at exocytosis.     

Determination of urinary steroid sulfate metabolites using ion paired extraction

The need for laboratories accredited by the World Anti-Doping Agency (WADA) to develop methods of analysis for steroids excreted primarily as their sulfate conjugates has faced significant analytical challenges. One of the issues relates to the extraction of these metabolites from urine in a relatively pure state. The use of (-)-N,N-dimethylephedrinium bromide as an ion pairing reagent was optimised to produce a method that is selective for the extraction of steroid sulfates prior to GC-MS or LC-MS analysis, with minimal contributions from the urine matrix. The recovery of androsterone from its sulfate conjugate was determined to be 67% with a relative quantitative uncertainty of +/-14% (k = 2).     

An olfactory subsystem that mediates high-sensitivity detection of volatile amines

Olfactory stimuli are detected by over 1,000 odorant receptors in mice, with each receptor being mapped to specific glomeruli in the olfactory bulb. The trace amine-associated receptors (TAARs) are a small family of evolutionarily conserved olfactory receptors whose contribution to olfaction remains enigmatic. Here, we show that a majority of the TAARs are mapped to a discrete subset of glomeruli in the dorsal olfactory bulb of the mouse. This TAAR projection is distinct from the previously described class I and class II domains, and is formed by a sensory neuron population that is restricted to express TAAR genes prior to choice. We also show that the dorsal TAAR glomeruli are selectively activated by amines at low concentrations. Our data uncover a hard-wired, parallel input stream in the main olfactory pathway that is specialized for the detection of volatile amines.     

eIF4E-binding protein regulation of mRNAs with differential 5'-UTR secondary structure: a polyelectrostatic model for a component of protein-mRNA interactions

Control of translation in eukaryotes is complex, depending on the binding of various factors to mRNAs. Available data for subsets of mRNAs that are translationally up- and down-regulated in yeast eIF4E-binding protein (4E-BP) deletion mutants are coupled with reported mRNA secondary structure measurements to investigate whether 5'-UTR secondary structure varies between the subsets. Genes with up-regulated translational efficiencies in the caf20Δ mutant have relatively high averaged 5'-UTR secondary structure. There is no apparent wide-scale correlation of RNA-binding protein preferences with the increased 5'-UTR secondary structure, leading us to speculate that the secondary structure itself may play a role in differential partitioning of mRNAs between eIF4E/4E-BP repression and eIF4E/eIF4G translation initiation. Both Caf20p and Eap1p contain stretches of positive charge in regions of predicted disorder. Such regions are also present in eIF4G and have been reported to associate with mRNA binding. The pattern of these segments, around the canonical eIF4E-binding motif, varies between each 4E-BP and eIF4G. Analysis of gene ontology shows that yeast proteins containing predicted disordered segments, with positive charge runs, are enriched for nucleic acid binding. We propose that the 4E-BPs act, in part, as differential, flexible, polyelectrostatic scaffolds for mRNAs.     

Nitric oxide-evoked transient kinetics of cyclic GMP in vascular smooth muscle cells

Cyclic-3',5'-guanosine monophosphate (cGMP) mediates the intracellular signaling cascade responsible for the nitric oxide (NO) initiated relaxation of vascular smooth muscle (VSM). However, the temporal dynamics, including the regulation of cGMP turnover, are largely unknown. Here we report new mechanistic insights into the kinetics of cGMP synthesis and hydrolysis in primary VSM cells by utilizing FRET-based cGMP-indicators [A. Honda, S.R. Adams, C.L. Sawyer, V. Lev-Ram, R.Y. Tsien, W.R. Dostmann, Proc. Natl. Acad. Sci. U S A 98 (5) (2001) 2437.]. First, 2-(N,N-Diethylamino)-diazenolate 2-oxide (DEA/NO) and 2,2'-(Hydroxynitrosohydrazono)-bis-ethanimine (DETA/NO) induced NO-concentration dependent, transient cGMP responses ("peaks") irrespective of their rates of NO release. The kinetic characteristics of these cGMP peaks were governed by the concerted action of the NO-sensitive guanylyl cyclase (GC) and phosphodiesterase type V (PDE5) as shown by their respective inhibition using 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one (ODQ) and Sildenafil. These responses occurred in the presence of moderately elevated cGMP (5-15% FRET ratio), and thus activated PKG and phosphorylated PDE5, suggesting a prominent role for GC in the maintenance and termination of cGMP peaks. Furthermore, cGMP transients could be elicited repeatedly without apparent desensitization of GC or by suppression of cGMP via long-term PDE5 activity. These results demonstrate a continuous sensitivity of the NO/cGMP signaling system, inherent to the phasic nature of smooth muscle physiology.     

Obesity and skill attainment in early childhood

This paper investigates the association between obesity and skill attainment in early childhood (aged 2-3 years). Data from the German Socio-Economic Panel Study are used to estimate models of developmental functioning in four critical areas (verbal skills, activities of daily living, motor skills, and social skills) as a function of various measures of weight (including body mass index and obesity) controlling for a rich set of child, parent, and family characteristics. The findings indicate that, among boys, obesity is associated with reduced verbal skills, social skills, motor skills, and activities of daily living. Among girls, obesity is associated with reduced verbal skills. Further investigations show that the correlations exist even for those preschool children who spend no time in day care, which implies that the correlations cannot be due solely to discrimination by teachers, classmates, or day care providers.     

Disuccinimidyl suberate cross-linked ricin does not inhibit cell-free protein synthesis

Ricin was reacted with disuccinimidyl suberate, to yield a molecule in which the A and B chains were covalently cross-linked through a non-reducible bond. After purification, this cross-linked ricin analog was unable to inhibit protein synthesis in a cell-free translation system from rat liver. In contrast, after modification with the cross-linking agent the isolated ricin A chain maintained its inhibitory activity. These results support the view that ricin must be cleaved into its constituent polypeptide chains to elicit its toxicity, and suggest that reduction of the disulfide bond alone is not sufficient for ribosome inactivation $\text{in}\text{vitro}$.