A horizontal alignment tool for numerical trend discovery in sequence data: application to protein hydropathy.

PMC3794901An algorithm is presented that returns the optimal pairwise gapped alignment of two sets of signed numerical sequence values. One distinguishing feature of this algorithm is a flexible comparison engine (based on both relative shape and absolute similarity measures) that does not rely on explicit gap penalties. Additionally, an empirical probability model is developed to estimate the significance of the returned alignment with respect to randomized data. The algorithm's utility for biological hypothesis formulation is demonstrated with test cases including database search and pairwise alignment of protein hydropathy. However, the algorithm and probability model could possibly be extended to accommodate other diverse types of protein or nucleic acid data, including positional thermodynamic stability and mRNA translation efficiency. The algorithm requires only numerical values as input and will readily compare data other than protein hydropathy. The tool is therefore expected to complement, rather than replace, existing sequence and structure based tools and may inform medical discovery, as exemplified by proposed similarity between a chlamydial ORFan protein and bacterial colicin pore-forming domain. The source code, documentation, and a basic web-server application are available.JH Libraries Open Access Fun

Dynamic Changes in Arteriovenous Malformations (AVMs): Spontaneous Growth and Resolution of AVM-Associated Aneurysms in Two Pediatric Patients

Arteriovenous malformations (AVMs) of the central nervous system are dynamic lesions that can change with time. One of the most clinically important concerns is the development and potential rupture of AVM-associated aneurysms. In this report, we review pediatric cases of de novo development of AVM-associated aneurysms in 2 children and present the relevant clinical and radiographic records. These 2 cases, coupled with a review of the current literature, offer insight into the risks of AVMs in children and underline the importance of timely treatment of appropriate cases

Segregation of glutamatergic and cholinergic transmission at the mixed motoneuron Renshaw cell synapse

In neonatal mice motoneurons excite Renshaw cells by releasing both acetylcholine (ACh) and glutamate. These two neurotransmitters activate two types of nicotinic receptors (nAChRs) (the homomeric α7 receptors and the heteromeric α*ß* receptors) as well as the two types of glutamate receptors (GluRs) (AMPARs and NMDARs). Using paired recordings, we confirm that a single motoneuron can release both transmitters on a single post-synaptic Renshaw cell. We then show that co-transmission is preserved in adult animals. Kinetic analysis of miniature EPSCs revealed quantal release of mixed events associating AMPARs and NMDARs, as well as α7 and α*ß* nAChRs, but no evidence was found for mEPSCs associating nAChRs with GluRs. Bayesian Quantal Analysis (BQA) of evoked EPSCs showed that the number of functional contacts on a single Renshaw cell is more than halved when the nicotinic receptors are blocked, confirming that the two neurotransmitters systems are segregated. Our observations can be explained if ACh and glutamate are released from common vesicles onto spatially segregated post-synaptic receptors clusters, but a pre-synaptic segregation of cholinergic and glutamatergic release sites is also possible