T7 Exonuclease (GENE 6) is Necessary for Molecular Recombination of Bacteriophage T7

The role of T7-induced exonuclease (gene 6) in molecular recombination was studied by examining the fate of parental DNA during parental-to-progeny recombination. The method used was to compare infections with T7(+), T7am-6-233 (am gene 6), or T7ts6-136 (ts gene 6) under permissive and nonpermissive conditions. CsCl density gradient analysis of replicative DNA indicated that T7 exonuclease is necessary for recombination to occur, i.e., in the absence of the exonuclease the parental DNA replicated continuously as a hybrid molecule and did not recombine. Further studies under conditions where replicative DNA was denatured and analyzed by CsCl density gradient centrifugation indicated that the exonuclease is also needed for a limited amount of covalent repair of recombinants. A repair function for the T7-induced exonuclease is also suggested by results obtained from alkaline sucrose gradient analysis of replicative DNA. Under conditions nonpermissive for the exonuclease, discontinuities in the DNA accumulated during infection by T7am6-233 or by T7ts6-136.     

Effects of anesthetic agents on brain blood oxygenation level revealed with ultra-high field MRI

During general anesthesia it is crucial to control systemic hemodynamics and oxygenation levels. However, anesthetic agents can affect cerebral hemodynamics and metabolism in a drug-dependent manner, while systemic hemodynamics is stable. Brain-wide monitoring of this effect remains highly challenging. Because T(2)*-weighted imaging at ultra-high magnetic field strengths benefits from a dramatic increase in contrast to noise ratio, we hypothesized that it could monitor anesthesia effects on brain blood oxygenation. We scanned rat brains at 7T and 17.2T under general anesthesia using different anesthetics (isoflurane, ketamine-xylazine, medetomidine). We showed that the brain/vessels contrast in T(2)*-weighted images at 17.2T varied directly according to the applied pharmacological anesthetic agent, a phenomenon that was visible, but to a much smaller extent at 7T. This variation is in agreement with the mechanism of action of these agents. These data demonstrate that preclinical ultra-high field MRI can monitor the effects of a given drug on brain blood oxygenation level in the absence of systemic blood oxygenation changes and of any neural stimulation.     

Tracking the unconscious generation of free decisions using ultra-high field fMRI

Recently, we demonstrated using functional magnetic resonance imaging (fMRI) that the outcome of free decisions can be decoded from brain activity several seconds before reaching conscious awareness. Activity patterns in anterior frontopolar cortex (BA 10) were temporally the first to carry intention-related information and thus a candidate region for the unconscious generation of free decisions. In the present study, the original paradigm was replicated and multivariate pattern classification was applied to functional images of frontopolar cortex, acquired using ultra-high field fMRI at 7 Tesla. Here, we show that predictive activity patterns recorded before a decision was made became increasingly stable with increasing temporal proximity to the time point of the conscious decision. Furthermore, detailed questionnaires exploring subjects' thoughts before and during the decision confirmed that decisions were made spontaneously and subjects were unaware of the evolution of their decision outcomes. These results give further evidence that FPC stands at the top of the prefrontal executive hierarchy in the unconscious generation of free decisions.     

Screening of substrate peptide sequences for tissue-type transglutaminase (TGase 2) using T7 phage cDNA library

Transglutaminase (TGase) is a family of enzymes that catalyzes cross-linking reaction between glutamine- and lysine residue of substrate proteins in several mammalian biological events. Substrate proteins for TGase and their physiological relevance have been still in research, continuously expanding. In this study, we have established a novel screening system that enables identification of cDNA sequence encoding favorable primary structure as a substrate for tissue-type transglutaminase (TGase 2), a multifunctional and ubiquitously expressing isozyme. By the screening, we identified several T7 phage clones that displayed substrate peptides for TGase 2 as a translated product from human brain cDNA library. Among the selected clones, the C-terminal region of IKAP, IkappaB kinase complex associated protein, appeared as a highly reactive substrate sequence for TGase 2. This system will open possibility of rapid identification of substrate sequences for transglutaminases at a genetic level.     

In Vivo 7T MRI of the Non-Human Primate Brainstem

Structural brain imaging provides a critical framework for performing stereotactic and intraoperative MRI-guided surgical procedures, with procedural efficacy often dependent upon visualization of the target with which to operate. Here, we describe tools for in vivo, subject-specific visualization and demarcation of regions within the brainstem. High-field 7T susceptibility-weighted imaging and diffusion-weighted imaging of the brain were collected using a customized head coil from eight rhesus macaques. Fiber tracts including the superior cerebellar peduncle, medial lemniscus, and lateral lemniscus were identified using high-resolution probabilistic diffusion tractography, which resulted in three-dimensional fiber tract reconstructions that were comparable to those extracted from sequential application of a two-dimensional nonlinear brain atlas warping algorithm. In the susceptibility-weighted imaging, white matter tracts within the brainstem were also identified as hypointense regions, and the degree of hypointensity was age-dependent. This combination of imaging modalities also enabled identifying the location and extent of several brainstem nuclei, including the periaqueductal gray, pedunculopontine nucleus, and inferior colliculus. These clinically-relevant high-field imaging approaches have potential to enable more accurate and comprehensive subject-specific visualization of the brainstem and to ultimately improve patient-specific neurosurgical targeting procedures, including deep brain stimulation lead implantation.     

Deformation and recovery of cartilage in the intact hip under physiological loads using 7 T MRI

Accurate measurement of cartilage deformation in loaded cadaver hip joints could be a valuable tool to answer clinically relevant research questions. MRI is a promising tool, but its use requires an understanding of cartilage deformation and recovery properties in the intact hip. Our objective was to answer the following questions: (1) How long does it take for hip cartilage to reach a deformed steady-state thickness distribution under simulated physiological load, and how much does the cartilage deform? (2) How long does it take for hip cartilage to return to the original cartilage thickness distribution once the load is removed?MethodsFive human hip specimens were axially loaded to 1980 N in a 7 T MR scanner and scanned every 15 min throughout loading. One specimen was scanned every hour throughout recovery from load. One repeatability specimen was loaded and scanned every day for 4 days. Hip cartilage was segmented as a single unit and thickness was measured radially.ResultsThe hip cartilage reached a steady-state thickness distribution after 225 min of load, and 16.5 h of recovery. Mean strain after 225 min of load was 30.9%. The repeatability specimen showed an average day-to-day change in mean cartilage thickness of 0.10 mm over 4 days of data collection. The amount of deformation (0.96 mm) was far greater than the image resolution (0.11 mm) and error due to repeatability (0.10 mm).ConclusionUsing an ex vivo model, this method has potential for assessing changes in hip cartilage strain due to injury or surgical intervention.     

Comprehensive in vivo mapping of the human basal ganglia and thalamic connectome in individuals using 7T MRI

Basal ganglia circuits are affected in neurological disorders such as Parkinson's disease (PD), essential tremor, dystonia and Tourette syndrome. Understanding the structural and functional connectivity of these circuits is critical for elucidating the mechanisms of the movement and neuropsychiatric disorders, and is vital for developing new therapeutic strategies such as deep brain stimulation (DBS). Knowledge about the connectivity of the human basal ganglia and thalamus has rapidly evolved over recent years through non-invasive imaging techniques, but has remained incomplete because of insufficient resolution and sensitivity of these techniques. Here, we present an imaging and computational protocol designed to generate a comprehensive in vivo and subject-specific, three-dimensional model of the structure and connections of the human basal ganglia. High-resolution structural and functional magnetic resonance images were acquired with a 7-Tesla magnet. Capitalizing on the enhanced signal-to-noise ratio (SNR) and enriched contrast obtained at high-field MRI, detailed structural and connectivity representations of the human basal ganglia and thalamus were achieved. This unique combination of multiple imaging modalities enabled the in-vivo visualization of the individual human basal ganglia and thalamic nuclei, the reconstruction of seven white-matter pathways and their connectivity probability that, to date, have only been reported in animal studies, histologically, or group-averaged MRI population studies. Also described are subject-specific parcellations of the basal ganglia and thalamus into sub-territories based on their distinct connectivity patterns. These anatomical connectivity findings are supported by functional connectivity data derived from resting-state functional MRI (R-fMRI). This work demonstrates new capabilities for studying basal ganglia circuitry, and opens new avenues of investigation into the movement and neuropsychiatric disorders, in individual human subjects.     

Site-specific in vivo targeting of magnetoliposomes using externally applied magnetic field

Human serum albumin labeled with technetium-99m was encapsulated together with magnetite particles into phosphatidylcholine/cholesterol liposomes. In order to investigate the stability of this complex and its ability to be used for magnetic drug targeting, the in-vivo distribution after intravenous administration in rats was estimated. For in-vivo targeting an SmCo permanent magnet with intensity approximately 0.35 T was attached near the right kidney. Difference between the relative radioactivity in the magnetically targeted right kidney (25.92+/-5.84%) and non-targeted left kidney (0.93+/-0.05%) is sufficiently high for relevant clinical applications.     

Solvent effects on model d(CG·G)7 and d(TA·T)7 DNA triple helices

Using free energy molecular mechanics, we find that the molecular effects of solvent are critical in determining relative stabilities in DNA triple helices or triplexes. The continuum solvent model is unable to differentiate the thermodynamics reflecting the basic solvation differences around the occupied major groove in triplexes. In order to avoid the local minimum problem, which is a major limitation of any modeling study, we started our computations with multiple structures rather than relying on the optimization of a single reference structure. By constructing triplex models with different initial helical twists, helical rises, and sugar-pucker permutations, we explore the potential surface and the structural preference with respect to these variations. We find that in order to accommodate a third strand in triplex formation, the backbone geometry of the B-DNA duplex target has to be adjusted into A-DNA-like form with a deep major groove. This is achieved by concerted adjustment in torsions β, ε, and ζ around the phosphate groups. However, the sugar pucker displays a more rich variation, resulting in conformations not usually associated with the canonical duplex structures. © 1995 John Wiley & Sons, Inc.     

A prospective comparative dosimetric study between diffusion weighted MRI (DWI) & T2-weighted MRI (T2W) for target delineation and planning in cervical cancer brachytherapy

AimTo evaluate the difference between GTVBT (Gross Tumor Volume at Brachytherapy) and HR CTV (High Risk Clinical Tumor Volume) delineated with DWI and T2W MRI. To evaluate doses to organs at risk and targets from plans generated using T2W and DWI.BackgroundFunctional imaging with DWI can improve cervical tumor distinction as it is more sensitive than T2W MRI even in detecting parametrial invasion. This study does a dosimetric comparison between a T2W and DWI based plan.MethodsFifty carcinoma cervix patients were subjected to MRI based brachytherapy. T2W and a diffusion weighted sequence were acquired. Target delineation and brachytherapy planning was done on both T2W and DWI. Standard DVH parameters were recorded and the treatment was given using the plan generated from T2W images.ResultsGTVBT and HRCTV contours on DWI were different when compared with T2W. Mean GTVBT volume on T2W and DWI was 5.25 and 5.23, respectively (p value 0.8). Mean HRCTV on T2W and DWI was 28.3 and 27 cc, respectively (p value 0.003). Planning on the above volumes resulted in a superior coverage in terms of HRCTV D90 and D100 for DWI based plan, HRCTV D90 — 735.1 and 741 cGy for T2W and DWI, respectively (p value 0.006), HRCTV D100 — 441.05 and 444.5 for T2W and DWI plans, respectively (p value = 0.006). Doses to the OAR were not significantly increased.ConclusionGEC ESTRO based contouring guidelines cover all the functionally abnormal areas on DWI. DWI should only be used as a supplement to T2W for contouring target volumes.     

Continuous flow solid (gel) phase peptide synthesis using unsupported ultra-high load polymers.

A simple, manually operated, continuous flow apparatus is described for solid (gel) phase peptide synthesis. The approach uses an unsupported phenolic bead form core network at an initial matrix loading of 5 mmol g-1, the theoretical maximum. The synthesis is performed in a flow reactor under low pressure conditions. "Layered displacement" of reagent solutions and washing solvents is an essential feature that has been developed to facilitate efficient peptide synthesis. The usefulness of the present system in conjunction with N alpha Boc protected amino acids is illustrated by the syntheses of [Leu5]-enkephalin and dermorphin. The potential for scale up synthesis has also been investigated.     

Feasibility of noninvasive evaluation of biophysical properties of tissue-engineered cartilage by using quantitative MRI

The application of tissue-engineered cartilage in a clinical setting requires a noninvasive method to assess the biophysical and biochemical properties of the engineered cartilage. Since articular cartilage is composed of 70-80% water and has dense extracellular matrixes (ECM), it is considered that the condition of the water molecules in the tissue is correlated with its biomechanical property. Therefore, magnetic resonance imaging (MRI) represents a potential approach to assess the biophysical property of the engineered cartilage. In this study, we test the hypothesis that quantitative MRI can be used as a noninvasive assessment method to assess the biophysical property of the engineered cartilage. To reconstruct a model of cartilaginous tissue, chondrocytes harvested from the humeral head of calves were embedded in an agarose gel and cultured in vitro up to 4 weeks. Equilibrium Young's moduli were determined from the stress relaxation tests. After mechanical testing, MRI-derived parameters (longitudinal relaxation time T1, transverse relaxation time T2, and water self-diffusion coefficient D) were measured. The equilibrium Young's modulus of the engineered cartilage showed a tendency to increase with an increase in the culture time, whereas T1 and D decreased. Based on a regression analysis, T1 and D showed a strong correlation with the equilibrium Young's modulus. The results showed that T1 and D values derived from the MRI measurements could be used to noninvasively monitor the biophysical properties of the engineered cartilage.     

SCF(Fbw7) modulates the NFkB signaling pathway by targeting NFkB2 for ubiquitination and destruction

The NFkB/Rel family of proteins play critical roles in a variety of cellular processes. Thus, their physiological activation is tightly controlled. Recently, the NFkB2/p100 precursor has been characterized as the fourth IkB type of suppressor for NFkB. However, the molecular mechanism(s) underlying regulated destruction of NFkB2 remains largely unknown. Here, we report that, unlike other IkBs, ubiquitination and destruction of NFkB2 are governed by SCF(Fbw7) in a GSK3-dependent manner. In Fbw(7-/-) cells, elevated expression of NFkB2/p100 leads to a subsequent reduction in NFkB signaling pathways and elevated sensitivity to TNFa-induced cell death. Reintroducing wild-type Fbw7, but not disease-derived mutant forms of Fbw7, rescues NFkB activity. Furthermore, T cell-specific depletion of Fbw7 also leads to reduced NFkB activity and perturbed T cell differentiation. Therefore, our work identifies Fbw7 as a physiological E3 ligase controlling NFkB20s stability. It further implicates that Fbw7 might exert its tumor-suppressor function by regulating NFkB activity.     

Src-like adaptor protein down-regulates T cell receptor (TCR)-CD3 expression by targeting TCRzeta for degradation

Src-like adaptor protein (SLAP) down-regulates expression of the T cell receptor (TCR)-CD3 complex during a specific stage of thymocyte development when the TCR repertoire is selected. Consequently, SLAP-/- thymocytes display alterations in thymocyte development. Here, we have studied the mechanism of SLAP function. We demonstrate that SLAP-deficient thymocytes have increased TCRzeta chain expression as a result of a defect in TCRzeta degradation. Failure to degrade TCRzeta leads to an increased pool of fully assembled TCR-CD3 complexes that are capable of recycling back to the cell surface. We also provide evidence that SLAP functions in a pathway that requires the phosphorylated TCRzeta chain and the Src family kinase Lck, but not ZAP-70 (zeta-associated protein of 70 kD). These studies reveal a unique mechanism by which SLAP contributes to the regulation of TCR expression during a distinct stage of thymocyte development.     

Cranial MRI of small rodents using a clinical MR scanner

Increasing numbers of small animal models are in use in the field of neuroscience research. Magnetic resonance imaging (MRI) provides an excellent method for non-invasive imaging of the brain. Using three-dimensional (3D) MR sequences allows lesion volumetry, e.g. for the quantification of tumor size. Specialized small-bore animal MRI scanners are available for high-resolution MRI of small rodents' brain, but major drawbacks of this dedicated equipment are its high costs and thus its limited availability. Therefore, more and more research groups use clinical MR scanners for imaging small animal models. But to achieve a reasonable spatial resolution at an acceptable signal-to-noise ratio with these scanners, some requirements concerning sequence parameters have to be matched. Thus, the aim of this paper was to present in detail a method how to perform MRI of small rodents brain using a standard clinical 1.5 T scanner and clinically available radio frequency coils to keep material costs low and to circumvent the development of custom-made coils.     

Enzyme field effect transistor (ENFET) for estimation of triglycerides using magnetic nanoparticles

Ion-selective field effect transistor (ISFET) is a robust platform to develop biosensors. A variety of methods are used including covalent attachment or polymer entrapment, to associate enzymes or antibodies to the gate surface of a FET. We have employed a novel method of retaining the enzyme molecules at the gate surface by immobilizing the enzyme on magnetic nickelferrite nanoparticles and applying a permanent magnet below the gate of the FET. We were able to estimate the triglyceride concentrations in the range of 0.1–1.5% by immobilizing a thermostable lipase on nanoparticles. Tributyrin, trioctanoate and triolein have given similar results. The reaction volume could be scaled down to 0.2 ml without a loss in slope or sensitivity. Ionic strength (>150 mM NaCl) has a strong influence on the sensitivity of the measurement. The advantages of this configuration of enzyme biosensor are reduction of mass transfer problems, increasing the amount of enzyme at the gate surface besides providing an opportunity to use a single FET device for multiple analyte detection.     

Proteolysis targeting chimeras (PROTACs) for epigenetics research

Proteolysis targeting chimeras (PROTACs) are heterobifunctional molecules and allow selective protein degradation by addressing the natural ubiquitin proteasome system. As this new strategy of chemically induced protein degradation can serve as a biological tool and provides new possibilities for drug discovery, it has been applied to a variety of targets including (nuclear) receptors, kinases, and epigenetic proteins. A lot of PROTACs have already been designed in the field of epigenetics, and their synthesis and characterization highly contributed to structural optimization and improved mechanistic understanding of these molecules. In this review, we will discuss and summarize recent advances in PROTAC discovery with focus on epigenetic targets.