Stochastic segmentation models for array-based comparative genomic hybridization data analysis

Array-based comparative genomic hybridization (array-CGH) is a high throughput, high resolution technique for studying the genetics of cancer. Analysis of array-CGH data typically involves estimation of the underlying chromosome copy numbers from the log fluorescence ratios and segmenting the chromosome into regions with the same copy number at each location. We propose for the analysis of array-CGH data, a new stochastic segmentation model and an associated estimation procedure that has attractive statistical and computational properties. An important benefit of this Bayesian segmentation model is that it yields explicit formulas for posterior means, which can be used to estimate the signal directly without performing segmentation. Other quantities relating to the posterior distribution that are useful for providing confidence assessments of any given segmentation can also be estimated by using our method. We propose an approximation method whose computation time is linear in sequence length which makes our method practically applicable to the new higher density arrays. Simulation studies and applications to real array-CGH data illustrate the advantages of the proposed approach.     

Virtual screening and biophysical studies lead to HSP90 inhibitors

Heat shock protein 90 (HSP90) is a molecular chaperone that plays important functional roles in cells. The chaperone activity of HSP90 is regulated by the hydrolysis of ATP at the protein’s N-terminal domain. HSP90, in particular the N-terminal domain, is a current inhibition target for therapeutic treatments of cancers. This paper describes an application of virtual screening, thermal shift assaying and protein NMR spectroscopy leading to the discovery of HSP90 inhibitors that contain the resorcinol structure. The resorcinol scaffold can be found in a class of HSP90 inhibitors that are currently undergoing clinical trials. The proved success of the resorcinol moiety in HSP90 inhibitors validates this combined virtual screen and biophysical technique approach, which may be applied for future inhibitor discovery work for HSP90 as well as other targets.     

Synthesis and photophysical properties of new fluorinated benzo[c]xanthene dyes as intracellular pH indicators.

Two new fluorinated benzo[c]xanthene dyes were synthesized by reaction of fluorinated 1,6-dihydroxynaphthalenes with 2,4- (and 2,5)-dicarboxy-3'-dimethylamino-2'-hydroxybenzophenone. The two critical fluorinated 1,6-dihydroxynaphthalene intermediates were prepared via a regioselective route. The fluorinated benzo[c]xanthene dyes exhibit desired lower pK(a) values (6.4 and 7.2, respectively) than their parent compound (pK(a)=7.5) while the pH-dependent dual-emission characteristics are well retained. Their cell-permeable esters have been prepared for intracellular applications.     

Quantitative measurement of spastic ankle joint stiffness using a manual device: A preliminary study

Quantitative measurement of ankle joint stiffness following stroke could prove useful in monitoring the progress of a rehabilitation programme. The objective of this study was to design a manual device for use in the clinical setting. Manual measurement of spastic ankle joint stiffness has historically been conducted using hand-held dynamometers or alternative devices, but some difficulties have been reported in controlling the velocity applied to the ankle during the measurement. In this study, a manually operated device was constructed with a footplate, a torquemeter and a potentiometer. It was mechanically designed to rotate around an approximated axis of the ankle joint and to measure ankle joint angular position and its corresponding resistive torque. Two stroke hemiplegic subjects pariticapted in a pilot study. The results suggested that difficulty in controlling the applied velocity might be complemented by presenting torque data as a function of peak angular velocity in each stretching cycle. Moreover, the results demonstrated that the device could potentially apply a wide range of angular velocities and provide potentially useful clinical information. Quantitative data successfully acquired using this method included the approximate ankle angular position, where the velocity-dependent characteristics of stiffness was notably initiated and its corresponding torque and velocity.     

Deciphering signaling control by phosphoproteome using mass spectrometry

Analysis of changes in genes and protein profiles provides invaluable information to understand the activities and functions of proteins. However, their activities are further regulated by post-translational modifications, such as glycosylation and phosphorylation. Cell growth and apoptotic pathways are good examples of demonstrating the roles of phosphorylation in activation of protein cascades upon stimulation.     

The neuronal receptor tyrosine kinase Alk is a target for longevity

Inhibition of signalling through several receptor tyrosine kinases (RTKs), including the insulin‐like growth factor receptor and its orthologues, extends healthy lifespan in organisms from diverse evolutionary taxa. This raises the possibility that other RTKs, including those already well studied for their roles in cancer and developmental biology, could be promising targets for extending healthy lifespan. Here, we focus on anaplastic lymphoma kinase (Alk), an RTK with established roles in nervous system development and in multiple cancers, but whose effects on aging remain unclear. We find that several means of reducing Alk signalling, including mutation of its ligand jelly belly (jeb), RNAi knock‐down of Alk, or expression of dominant‐negative Alk in adult neurons, can extend healthy lifespan in female, but not male, Drosophila. Moreover, reduced Alk signalling preserves neuromuscular function with age, promotes resistance to starvation and xenobiotic stress, and improves night sleep consolidation. We find further that inhibition of Alk signalling in adult neurons modulates the expression of several insulin‐like peptides, providing a potential mechanistic link between neuronal Alk signalling and organism‐wide insulin‐like signalling. Finally, we show that TAE‐684, a small molecule inhibitor of Alk, can extend healthy lifespan in Drosophila, suggesting that the repurposing of Alk inhibitors may be a promising direction for strategies to promote healthy aging.     

Human ZBP1 induces cell death‐independent inflammatory signaling via RIPK3 and RIPK1

ZBP1 is an interferon‐induced cytosolic nucleic acid sensor that facilitates antiviral responses via RIPK3. Although ZBP1‐mediated programmed cell death is widely described, whether and how it promotes inflammatory signaling is unclear. Here, we report a ZBP1‐induced inflammatory signaling pathway mediated by K63‐ and M1‐linked ubiquitin chains, which depends on RIPK1 and RIPK3 as scaffolds independently of cell death. In human HT29 cells, ZBP1 associated with RIPK1 and RIPK3 as well as ubiquitin ligases cIAP1 and LUBAC. ZBP1‐induced K63‐ and M1‐linked ubiquitination of RIPK1 and ZBP1 to promote TAK1‐ and IKK‐mediated inflammatory signaling and cytokine production. Inhibition of caspase activity suppressed ZBP1‐induced cell death but enhanced cytokine production in a RIPK1‐ and RIPK3 kinase activity‐dependent manner. Lastly, we provide evidence that ZBP1 signaling contributes to SARS‐CoV‐2‐induced cytokine production. Taken together, we describe a ZBP1‐RIPK3‐RIPK1‐mediated inflammatory signaling pathway relayed by the scaffolding role of RIPKs and regulated by caspases, which may induce inflammation when ZBP1 is activated below the threshold needed to trigger a cell death response.