Single-Molecule Mechanical Analysis of Strand Invasion in Human Telomere DNA

Telomeres are essential chromosome end capping structures that safeguard the genome from dangerous DNA processing events. DNA strand invasion occurs during vital transactions at telomeres, including telomere length maintenance by the alternative lengthening of telomeres (ALT) pathway. During telomeric strand invasion, a single-stranded guanine-rich (G-rich) DNA invades at a complementary duplex telomere repeat sequence, forming a displacement loop (D-loop) in which the displaced DNA consists of the same G-rich sequence as the invading single-stranded DNA. Single-stranded G-rich telomeric DNA readily folds into stable, compact, structures called G-quadruplexes (GQs) in vitro and is anticipated to form within the context of a D-loop; however, evidence supporting this hypothesis is lacking. Here, we report a magnetic tweezers assay that permits the controlled formation of telomeric D-loops (TDLs) within uninterrupted duplex human telomere DNA molecules of physiologically relevant lengths. Our results are consistent with a model wherein the displaced single-stranded DNA of a TDL fold into a GQ. This study provides new insight into telomere structure and establishes a framework for the development of novel therapeutics designed to target GQs at telomeres in cancer cells.

Responses of midbrain auditory neurons to two different environmental sounds-A new approach on cross-sound modeling

When modeling auditory responses to environmental sounds, results are satisfactory if both training and testing are restricted to datasets of one type of sound. To predict 'cross-sound' responses (i.e., to predict the response to one type of sound e.g., rat Eating sound, after training with another type of sound e.g., rat Drinking sound), performance is typically poor. Here we implemented a novel approach to improve such cross-sound modeling (single unit datasets were collected at the auditory midbrain of anesthetized rats). The method had two key features: (a) population responses (e.g., average of 32 units) instead of responses of individual units were analyzed; and (b) the long sound segment was first divided into short segments (single sound-bouts), their similarity was then computed over a new metric involving the response (called Stimulus Response Model map or SRM map), and finally similar sound-bouts (regardless of sound type) and their associated responses (peri-stimulus time histograms, PSTHs) were modelled. Specifically, a committee machine model (artificial neural networks with 20 stratified spectral inputs) was trained with datasets from one sound type before predicting PSTH responses to another sound type. Model performance was markedly improved up to 92%. Results also suggested the involvement of different neural mechanisms in generating the early and late responses to amplitude transients in the broad-band environmental sounds. We concluded that it is possible to perform rather satisfactory cross-sound modeling on datasets grouped together based on their similarities in terms of the new metric of SRM map.

Modeling complex responses of FM-sensitive cells in the auditory midbrain using a committee machine

Frequency modulation (FM) is an important building block of complex sounds that include speech signals. Exploring the neural mechanisms of FM coding with computer modeling could help understand how speech sounds are processed in the brain. Here, we modeled the single unit responses of auditory neurons recorded from the midbrain of anesthetized rats. These neurons displayed spectral temporal receptive fields (STRFs) that had multiple-trigger features, and were more complex than those with single-trigger features. Their responses have not been modeled satisfactorily with simple artificial neural networks, unlike neurons with simple-trigger features. To improve model performance, here we tested an approach with the committee machine. For a given neuron, the peri-stimulus time histogram (PSTH) was first generated in response to a repeated random FM tone, and peaks in the PSTH were segregated into groups based on the similarity of their pre-spike FM trigger features. Each group was then modeled using an artificial neural network with simple architecture, and, when necessary, by increasing the number of neurons in the hidden layer. After initial training, the artificial neural networks with their optimized weighting coefficients were pooled into a committee machine for training. Finally, the model performance was tested by prediction of the response of the same cell to a novel FM tone. The results showed improvement over simple artificial neural networks, supporting that trigger-feature-based modeling can be extended to cells with complex responses. This article is part of a Special Issue entitled Neural Coding 2012. This article is part of a Special Issue entitled Neural Coding 2012.

Modeling frequency modulated responses of midbrain auditory neurons based on trigger features and artificial neural networks

Frequency modulation (FM) is an important building block of communication signals for animals and human. Attempts to predict the response of central neurons to FM sounds have not been very successful, though achieving successful results could bring insights regarding the underlying neural mechanisms. Here we proposed a new method to predict responses of FM-sensitive neurons in the auditory midbrain. First we recorded single unit responses in anesthetized rats using a random FM tone to construct their spectro-temporal receptive fields (STRFs). Training of neurons in the artificial neural network to respond to a second random FM tone was based on the temporal information derived from the STRF. Specifically, the time window covered by the presumed trigger feature and its delay time to spike occurrence were used to train a finite impulse response neural network (FIRNN) to respond to this random FM. Finally we tested the model performance in predicting the response to another similar FM stimuli (third random FM tone). We found good performance in predicting the time of responses if not also the response magnitudes. Furthermore, the weighting function of the FIRNN showed temporal 'bumps' suggesting temporal integration of synaptic inputs from different frequency laminae. This article is part of a Special Issue entitled: Neural Coding.

Fine frequency-modulation trigger features of midbrain auditory neurons extracted by the progressive thresholding method--a preliminary study

Spectro-temporal receptive fields (STRFs) are commonly used to characterize response properties of central auditory neurons and for visualizing 'trigger features'. However, trigger features in STRF maps typically have a blurry appearance. Therefore it is unclear what details could be embedded in them. To investigate this, we developed a new method called 'progressive thresholding' to resolve fine structures in the STRFs, and applied the method to FM responses recorded from single units at the auditory midbrain of anesthetized rats. Random FM tones of a narrow frequency range (approximately 0.5 octave) were first presented to evoked spike responses at the cell's best frequency. Perispike modulating time waveforms collected (50 msec long, n = 1500 to 4000 tracings) were used to generate STRF based on spike-triggered-averaging. After supra-threshold areas of pixel counts had been determined through a step of progressive thresholding in the map, those peri-spike modulating waveforms passing through each area were dejittered systematically. At what seemed to be an optimal threshold, multiple trigger features (up to a maximum of 4 fine bands) were extracted from the initially simple-looking STRF. Results show that fine FM trigger features are present in STRFs and that they can be resolved with the present method of analysis.

Mechanisms and dynamics of mechanical strengthening in ligament-equivalent fibroblast-populated collagen matrices

We have measured the dynamics of extracellular matrix consolidation and strengthening by human dermal fibroblasts in hydrated collagen gels. Constraining matrix consolidation between two porous polyethylene posts held rigidly apart set up the mechanical stress which led to the formation of uniaxially oriented fibroblast-populated collagen matrices with a histology resembling a ligament. We measured the mechanical stiffness and tensile strength of these ligament equivalents (LEs) as a function of age at biweekly intervals up to 12 weeks in culture using a mechanical spectrometer customized for performing experiments under physiologic conditions. The LE load-strain curve changed as a function of LE age, increasing in stiffness and exhibiting less plastic-like behavior. At 12 weeks, LEs had acquired up to 30 times the breaking strength of 1-week-old LEs. Matrix strengthening occurred primarily through the formation of BAPN-sensitive, lysyl oxidase catalyzed crosslinks. Sulfated glycosaminoglycan (GAG) content increased monotonically with LE age, reaching levels that are characteristic of ligaments. Cells in the LEs actively incorporated [3H]proline and [35S]sulfate into the extracellular matrix. Over the first three weeks, DNA content increased rapidly but thereafter remained constant. This data represent the first documentation of strengthening kinetics for cell-assembled biopolymer gels and the results suggest that this LE tissue may be a valuable model for studying the cellular processes responsible for tissue growth, repair, and remodeling.