Purification of NADPH:cytochrome c (cytochrome P-450) reductase from hamster liver microsomes by detergent extraction and affinity chromatography

NADPH:cytochrome c (cytochrome P-450) reductase (Fp) from hamster liver microsomes has been purified to near homogeneity using a simple and rapid method. Microsomes were treated with the detergent Chaps (3-[(3-cholamidopropyl)dimethylammonio]propanesulfonic acid) in combination with 0.07% protamine sulfate and then centrifuged to pellet insoluble material. While over 60% of the total microsomal protein was solubilized, all Fp activity remained in the pellet. Fp was extracted from the Chaps-insoluble material using a combination of the detergents sodium cholate and Lubrol PX. This treatment resulted in a fivefold increase in Fp specific activity and allowed direct processing of the enriched Fp fraction by 2',5'-ADP agarose affinity chromatography. The purified Fp had a total flavin content of 23 nmol/mg protein (flavin adenine dinucleotide:flavin mononucleotide ratio = 1:1), a specific activity of 26,000 units/mg protein at 22 degrees C using cytochrome c as electron acceptor, and migrated as a single band on sodium-dodecyl sulfate-polyacrylamide gel electrophoresis with a relative molecular weight of 76,000. The purity, specific activity, and yield were nearly identical to results obtained when the flavoprotein was purified by conventional methods. This procedure eliminates the need for anion-exchange chromatography and allows for the rapid purification of large amounts of Fp suitable for use in studies concerning cytochrome P-450-mediated drug metabolism. Importantly, this method is equally effective when used to purify Fp from rat liver microsomes.     

Notch Is Required in Adult Drosophila Sensory Neurons for Morphological and Functional Plasticity of the Olfactory Circuit

Olfactory receptor neurons (ORNs) convey odor information to the central brain, but like other sensory neurons were thought to play a passive role in memory formation and storage. Here we show that Notch, part of an evolutionarily conserved intercellular signaling pathway, is required in adult Drosophila ORNs for the structural and functional plasticity of olfactory glomeruli that is induced by chronic odor exposure. Specifically, we show that Notch activity in ORNs is necessary for the odor specific increase in the volume of glomeruli that occurs as a consequence of prolonged odor exposure. Calcium imaging experiments indicate that Notch in ORNs is also required for the chronic odor induced changes in the physiology of ORNs and the ensuing changes in the physiological response of their second order projection neurons (PNs). We further show that Notch in ORNs acts by both canonical cleavage-dependent and non-canonical cleavage-independent pathways. The Notch ligand Delta (Dl) in PNs switches the balance between the pathways. These data define a circuit whereby, in conjunction with odor, N activity in the periphery regulates the activity of neurons in the central brain and Dl in the central brain regulates N activity in the periphery. Our work highlights the importance of experience dependent plasticity at the first olfactory synapse.     

Mechanistic basis for RAG discrimination between recombination sites and the off-target sites of human lymphomas

During V(D)J recombination, RAG targeting to correct sites versus off-target sites relies on both DNA sequence features and on chromatin marks. Kinetic analysis using the first highly active full-length purified RAG1/RAG2 complexes has now allowed us to define the important catalytic features of this complex. We found that the overall rate of nicking, but not hairpinning, is critical for the discrimination between correct (optimal) versus off-target (suboptimal) sites used in human T-cell lymphomas, and we show that the C-terminal portion of RAG2 is required for this. This type of kinetic analysis permits us to analyze only the catalytically active RAG complex, in contrast to all other methods, which are unavoidably confounded by mixture with inactive RAG complexes. Moreover, we can distinguish the two major features of any enzymatic catalysis: the binding constant (K(D)) and the catalytic turnover rate, k(cat). Beyond a minimal essential threshold of heptamer quality, further suboptimal heptamer deviations primarily reduce the catalytic rate constant k(cat) for nicking. Suboptimal nonamers reduce not only the binding of the RAG complex to the recombination site (K(D)) but also the catalytic rate constant, consistent with a tight interaction between the RAG complex and substrate during catalysis. These features explain many aspects of RAG physiology and pathophysiology.     

Wrist and digital joint motion produce unique flexor tendon force and excursion in the canine forelimb

The force and excursion within the canine digital flexor tendons were measured during passive joint manipulations that simulate those used during rehabilitation after flexor tendon repair and during active muscle contraction, simulating the active rehabilitation protocol. Tendon force was measured using a small buckle placed upon the tendon while excursion was measured using a suture marker and video analysis method. Passive finger motion imposed with the wrist flexed resulted in dramatically lower tendon force (approximately 5 N) compared to passive motion imposed with the wrist extended (approximately 17 N). Lower excursions were seen at the level of the proximal interphalangeal joint with the wrist flexed (approximately 1.5 mm) while high excursion was observed when the wrist was extended or when synergistic finger and wrist motion were imposed (approximately 3.5 mm). Bivariate discriminant analysis of both force and excursion data revealed a natural clustering of the data into three general mechanical paradigms. With the wrist extended and with either one finger or four fingers manipulated, tendons experienced high loads of approximately 1500 g and high excursions of approximately 3.5 mm. In contrast, the same manipulations performed with the wrist flexed resulted in low tendon forces (4-8 N) and low tendon excursions of approximately 1.5 mm. Synergistic wrist and finger manipulation provided the third paradigm where tendon force was relatively low (approximately 4 N) but excursion was as high as those seen in the groups which were manipulated with the wrist extended. Active muscle contraction produced a modest tendon excursion (approximately 1 mm) and high or low tendon force with the wrist extended or flexed, respectively. These data provide the basis for experimentally testable hypotheses with regard to the factors that most significantly affect functional recovery after digital flexor tendon injury and define the normal mechanical operating characteristics of these tendons.     

A novel muscle biopsy clamp yields accurate in vivo sarcomere length values

The measurement of in vivo muscle sarcomere length facilitates the definition of in vivo muscle functional properties and comparison of muscle designs amongst functional muscle groups. In vivo sarcomere lengths are available for just a handful of human muscles, largely due to the technical challenges associated with their measurement. The purpose of this report was to develop and test a muscle biopsy clamp that can quickly and accurately measure in vivo muscle sarcomere length. To test the device, muscle biopsies (n=23) were removed from the tibialis anterior muscles of New Zealand White rabbits immediately after sarcomere length measurements were made using laser diffraction. The muscle biopsy contained within the clamp was immediately fixed in Formalin for subsequent sarcomere length measurement. Comparisons of clamp-based and diffraction-based sarcomere lengths demonstrated excellent agreement between the two techniques, especially when the biopsy was obtained at relatively long lengths (above 2.6 μm). Given the intraoperative speed and simplicity of this technique and the relatively low-cost of the biopsy clamp, this method of measuring muscle sarcomere length should help investigators generate much-needed in vivo muscle structural and functional data.     

DNA-PKcs regulates a single-stranded DNA endonuclease activity of Artemis

Human nuclease Artemis belongs to the metallo-beta-lactamase protein family. It acquires double-stranded DNA endonuclease activity in the presence of DNA-PKcs. This double-stranded DNA endonuclease activity is critical for opening DNA hairpins in V(D)J recombination and is thought to be important for processing overhangs during the nonhomologous DNA end joining (NHEJ) process. Here we show that purified human Artemis exhibits single-stranded DNA endonuclease activity. This activity is proportional to the amount of highly purified Artemis from a gel filtration column. The activity is stimulated by DNA-PKcs and modulated by purified antibodies raised against Artemis. Moreover, the divalent cation-dependence and sequence-dependence of this single-stranded endonuclease activity is the same as the double-stranded DNA endonuclease activity of Artemis:DNA-PKcs. These findings further expand the range of DNA substrates upon which Artemis and Artemis:DNA-PKcs can act. The findings are discussed in the context of NHEJ.     

Fabrication of silicon nanowire devices for ultrasensitive, label-free, real-time detection of biological and chemical species

Detection and quantification of biological and chemical species are central to many areas of healthcare and the life sciences, ranging from diagnosing disease to discovery and screening of new drug molecules. Semiconductor nanowires configured as electronic devices have emerged as a general platform for ultra-sensitive direct electrical detection of biological and chemical species. Here we describe a detailed protocol for realizing nanowire electronic sensors. First, the growth of uniform, single crystal silicon nanowires, and subsequent isolation of the nanowires as stable suspensions are outlined. Second, fabrication of addressable nanowire device arrays is described. Third, covalent modification of the nanowire device surfaces with receptors is described. Fourth, an example modification and measurements of the electrical response from devices are detailed. The silicon nanowire (SiNW) devices have demonstrated applications for label-free, ultrasensitive and highly-selective real-time detection of a wide range of biological and chemical species, including proteins, nucleic acids, small molecules and viruses.