Dmp1α Inhibits HER2/neu-Induced Mammary Tumorigenesis

Our recent study shows a pivotal role of Dmp1 in quenching hyperproliferative signals from HER2 to the Arf-p53 pathway as a safety mechanism to prevent breast carcinogenesis. To directly demonstrate the role of Dmp1 in preventing HER2/neu-driven oncogenic transformation, we established Flag-Dmp1α transgenic mice (MDTG) under the control of the mouse mammary tumor virus (MMTV) promoter. The mice were viable but exhibited poorly developed mammary glands with markedly reduced milk production; thus more than half of parous females were unable to support the lives of new born pups. The mammary glands of the MDTG mice had very low Ki-67 expression but high levels of Arf, Ink4a, p53, and p21^Cip1, markers of senescence and accelerated aging. In all strains of generated MDTG;neu mice, tumor development was significantly delayed with decreased tumor weight. Tumors from MDTG;neu mice expressed Flag-Dmp1α and Ki-67 in a mutually exclusive fashion indicating that transgenic Dmp1α prevented tumor growth in vivo. Genomic DNA analyses showed that the Dmp1α transgene was partially lost in half of the MDTG;neu tumors, and Western blot analyses showed Dmp1α protein downregulation in 80% of the cases. Our data demonstrate critical roles of Dmp1 in preventing mammary tumorigenesis and raise the possibility of treating breast cancer by restoring Dmp1α expression.     

Synthesis and biological activity of bi/tricyclic azasugars fused thiazolidin-4-one and thiazinan-4-one by microwave-assisted tandem Staudinger/aza-Wittig/cyclization

A convenient synthesis of novel bi/tricyclic azasugars fused thiazolidin-4-one and thiazinan-4-one by the one-pot tandem Staudinger/aza-Wittig/cyclization reaction under microwave radiation was demonstrated. The reactions were carried out with the azidosugar 1 and mercaptan acids via a key intermediate Schiff base and stereoselectively afforded the titled bi/tricyclic azasugars in good yield. All the dominant products were in the 1,2-trans form and the reaction stereoselectivity mainly depended upon the steric hindrance of the neighboring rigid cyclic isopropylidene groups on C-2, 3 which favors the exo-attack of the sulfur atom (in mercaptan acids) to the intermediate imine. The preliminary biological evaluation of the compounds 10-17 showed that compounds 10b, 11a, 12b, 14b, 16b, 17a, and 17b were found to active the natural killer (NK) cells significantly (immunopotentiating activity) and compounds 10a, 10b, 12a, 16b, and 17b exhibited weak inhibitory activity against β-glucosidase. Yet none of these tested compounds have obvious effects on T cell proliferation, or show inhibition against α-amylase and α-glucosidase.     

A Generic Model to Solve Tactical Planning Problems in Flexible Manufacturing Systems

This paper is an attempt to develop a generic modeling framework that addresses tactical planning problems of flexible manufacturing systems in a coherent manner. We propose a generic 0-1 mixed integer programming formulation, that integrates batching, loading, and routing problems with their critical aspects related to a system's performance. For this purpose, a thorough analysis is made to determine and relate system components, their attributes, and alternatives together with performance measures specific to tactical planning. This provided the justification to support our argument about generality of the model. A linear programming formulation is provided to approximate the mixed integer formulation proposed so as to overcome the problem's combinatorial complexity. The potential capability of the linear approximation proposed also is demonstrated via a small set of test problems.     

Large-scale de novo prediction of physical protein-protein association

Information about the physical association of proteins is extensively used for studying cellular processes and disease mechanisms. However, complete experimental mapping of the human interactome will remain prohibitively difficult in the near future. Here we present a map of predicted human protein interactions that distinguishes functional association from physical binding. Our network classifies more than 5 million protein pairs predicting 94,009 new interactions with high confidence. We experimentally tested a subset of these predictions using yeast two-hybrid analysis and affinity purification followed by quantitative mass spectrometry. Thus we identified 462 new protein-protein interactions and confirmed the predictive power of the network. These independent experiments address potential issues of circular reasoning and are a distinctive feature of this work. Analysis of the physical interactome unravels subnetworks mediating between different functional and physical subunits of the cell. Finally, we demonstrate the utility of the network for the analysis of molecular mechanisms of complex diseases by applying it to genome-wide association studies of neurodegenerative diseases. This analysis provides new evidence implying TOMM40 as a factor involved in Alzheimer's disease. The network provides a high-quality resource for the analysis of genomic data sets and genetic association studies in particular. Our interactome is available via the hPRINT web server at: www.print-db.org.     

Temporal but Not Spatial Variability during Gait Is Reduced after Selective Dorsal Rhizotomy in Children with Cerebral Palsy

Introduction

Variability in task output is a ubiquitous characteristic that results from non-continuous motor neuron firing during muscular force generation. However, variability can also be attributed to errors in control and coordination of the motor neurons themselves in diseases such as cerebral palsy (CP). Selective dorsal rhizotomy (SDR), a neurosurgical approach to sever sensory nerve roots, is thought to decrease redundant or excessive afferent signalling to intramedullary neurons. In addition to its demonstrated ability to reduce muscular spasticity, we hypothesised that SDR is able to decrease variability during gait, the most frequent functional motor activity of daily living.

Methods

Twelve CP children (aged 6.1±1.3yrs), who underwent SDR and performed gait analysis pre- and 12 months postoperatively, were compared to a control group of eleven typically developing (TD) children. Coefficients of variability as well as mean values were analysed for: temporal variables of gait, spatial parameters and velocity.

Results

Gait parameters of cadence (p = 0.006) and foot progression angle at mid-stance (p = 0.041) changed significantly from pre- to post-SDR. The variability of every temporal parameter was significantly reduced after SDR (p = 0.003–0.049), while it remained generally unchanged for the spatial parameters. Only a small change in gait velocity was observed, but variability in cadence was significantly reduced after SDR (p = 0.015). Almost all parameters changed with a tendency towards normal, but differences between TD and CP children remained in all parameters.

Discussion

The results confirm that SDR improves functional gait performance in children with CP. However, almost exclusively, parameters of temporal variability were significantly improved, leading to the conjecture that temporal variability and spatial variability may be governed independently by the motor cortex. As a result, temporal parameters of task performance may be more vulnerable to disruption, but also more responsive to treatment success of interventions such as SDR.     

Hierarchical Cascades of Instability Govern the Mechanics of Coiled Coils: Helix Unfolding Precedes Coil Unzipping

Coiled coils are a fundamental emergent motif in proteins found in structural biomaterials, consisting of α-helical secondary structures wrapped in a supercoil. A fundamental question regarding the thermal and mechanical stability of coiled coils in extreme environments is the sequence of events leading to the disassembly of individual oligomers from the universal coiled-coil motifs. To shed light on this phenomenon, here we report atomistic simulations of a trimeric coiled coil in an explicit water solvent and investigate the mechanisms underlying helix unfolding and coil unzipping in the assembly. We employ advanced sampling techniques involving steered molecular dynamics and metadynamics simulations to obtain the free-energy landscapes of single-strand unfolding and unzipping in a three-stranded assembly. Our comparative analysis of the free-energy landscapes of instability pathways shows that coil unzipping is a sequential process involving multiple intermediates. At each intermediate state, one heptad repeat of the coiled coil first unfolds and then unzips due to the loss of contacts with the hydrophobic core. This observation suggests that helix unfolding facilitates the initiation of coiled-coil disassembly, which is confirmed by our 2D metadynamics simulations showing that unzipping of one strand requires less energy in the unfolded state compared with the folded state. Our results explain recent experimental findings and lay the groundwork for studying the hierarchical molecular mechanisms that underpin the thermomechanical stability/instability of coiled coils and similar protein assemblies.     

Allele and genotype frequencies of CYP2B6 in a Turkish population

Increasing interest in cytochrome P450 2B6 (CYP2B6) genetic polymorphism was stimulated by revelations of a specific CYP2B6 genotype significantly affecting the metabolism of various drugs in common clinical use in terms of increasing drug efficacy and avoiding adverse drug reactions. The present study aimed to determine the frequencies of CYP2B6*4 CYP2B6*5, CYP2B6*6, CYP2B6*7 and CYP2B6*9 alleles in healthy Turkish individuals (n = 172). Frequencies of three single nucleotide polymorphisms were 516G>T (28 %), 785A>G (33 %), and 1459C>T (12 %). The frequencies of CYP2B6*1, *4, *5, *6, *7, and *9 alleles were 54.3 (95 % CI 49.04–59.56), 6.4 % (95 % CI 3.81–8.99), 11 % (95 % CI 7.69–14.31), 25.3 % (95 % CI 20.71–29.89), 0.87 % (95 % CI ?0.11–1.85) and 2.0 % (95 % CI 0.52–3.48), respectively. Allele *6 was more frequent (25.3 %) than the other variant alleles in Turkish subjects. The frequencies of CYP2B6*4, *5, *6, *7, and *9 alleles were similar to European populations but significantly different from that reported for Asian populations. This is the first study to document the frequencies of the CYP2B6*4, *5, *6, *7, *9 alleles in the healthy Turkish individuals and our results could provide clinically useful information on drug metabolism by CYP2B6 in Turkish population.