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Find video protocols related to scientific articles indexed in Pubmed.
An Extensive Antigenic Footprint Underpins Immunodominant TCR Adaptability against a Hypervariable Viral Determinant.
J. Immunol.
PUBLISHED: 10-29-2014
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Mutations in T cell epitopes are implicated in hepatitis C virus (HCV) persistence and can impinge on vaccine development. We recently demonstrated a narrow bias in the human TCR repertoire targeted at an immunodominant, but highly mutable, HLA-B*0801-restricted epitope ((1395)HSKKKCDEL(1403) [HSK]). To investigate if the narrow TCR repertoire facilitates CTL escape, structural and biophysical studies were undertaken, alongside comprehensive functional analysis of T cells targeted at the natural variants of HLA-B*0801-HSK in different HCV genotypes and quasispecies. Interestingly, within the TCR-HLA-B*0801-HSK complex, the TCR contacts all available surface-exposed residues of the HSK determinant. This broad epitope coverage facilitates cross-genotypic reactivity and recognition of common mutations reported in HCV quasispecies, albeit to a varying degree. Certain mutations did abrogate T cell reactivity; however, natural variants comprising these mutations are reportedly rare and transient in nature, presumably due to fitness costs. Overall, despite a narrow bias, the TCR accommodated frequent mutations by acting like a blanket over the hypervariable epitope, thereby providing effective viral immunity. Our findings simultaneously advance the understanding of anti-HCV immunity and indicate the potential for cross-genotype HCV vaccines.
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Sleep, Psychosocial Functioning, and Device-specific Adjustment in Patients with Implantable Cardioverter Defibrillators (ICDs).
Behav Sleep Med
PUBLISHED: 08-30-2014
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Rates of sleep disorders and associated adjustment were examined in patients with implantable cardioverter defibrillators (ICDs; n = 42; Mage = 61.57, SD = 12.60). One night of ambulatory polysomnography, 14 days of sleep diaries, and questionnaires (mood, sleepiness, fatigue, device acceptance) were administered. Controlling for ischemia, MANCOVA examined adjustment by sleep diagnosis. Apnea was most common (28.6%), followed by Insomnia (16.7%) and Comorbid Insomnia/Apnea (11.9%). Patients with insomnia reported poorer mood, greater sleepiness, and lower device acceptance than good sleepers; they also demonstrated poorer mood and less ICD device acceptance than patients with sleep apnea. Patients with comorbid insomnia/apnea also exhibited poorer mood and less ICD device acceptance than good sleepers; however, comorbid patients did not significantly differ from insomnia or apnea patients on any measure. Those with disordered sleep (regardless of type) reported greater fatigue than good sleepers. Assessment (and treatment) of difficulties with sleep, mood, fatigue, and device acceptance may be important for the comprehensive clinical management of ICD patients. Further research appears warranted.
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Nanoscale structure of the BMP antagonist chordin supports cooperative BMP binding.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 08-25-2014
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Bone morphogenetic proteins (BMPs) orchestrate key cellular events, such as proliferation and differentiation, in development and homeostasis. Extracellular antagonists, such as chordin, are essential regulators of BMP signaling. Chordin binds to BMPs blocking interaction with receptors, and cleavage by tolloid proteinases is thought to relieve this inhibition. A model has been previously proposed where chordin adopts a horseshoe-like arrangement enabling BMP binding cooperatively by terminal domains (1). Here, we present the nanoscale structure of human chordin using electron microscopy, small angle X-ray scattering, and solution-based biophysical techniques, which together show that chordin indeed has a compact horseshoe-shaped structure. Chordin variants were used to map domain locations within the chordin molecule. The terminal BMP-binding domains protrude as prongs from the main body of the chordin structure, where they are well positioned to interact with the growth factor. The spacing provided by the chordin domains supports the principle of a cooperative BMP-binding arrangement that the original model implied in which growth factors bind to both an N- and C-terminal von Willebrand factor C domain of chordin. Using binding and bioactivity assays, we compared full-length chordin with two truncated chordin variants, such as those produced by partial tolloid cleavage. Cleavage of either terminal domain has little effect on the affinity of chordin for BMP-4 and BMP-7 but C-terminal cleavage increases the efficacy of chordin as a BMP-4 inhibitor. Together these data suggest that partial tolloid cleavage is insufficient to ablate BMP inhibition and the C-terminal chordin domains play an important role in BMP regulation.
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Auto-adjusting Positive Airway Pressure Treatment for Sleep Apnea Diagnosed by Home Sleep Testing.
J Clin Sleep Med
PUBLISHED: 07-22-2014
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Compare auto-adjusting positive airway pressure (APAP) treatment with positive airway pressure (PAP) titration by polysomnography (PSG) followed by CPAP treatment in patients diagnosed with obstructive sleep apnea (OSA) by home sleep apnea testing (HSAT).
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Dual responsive pickering emulsion stabilized by poly[2-(dimethylamino)ethyl methacrylate] grafted cellulose nanocrystals.
Biomacromolecules
PUBLISHED: 07-14-2014
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A weak polyelectrolyte, poly[2-(dimethylamino)ethyl methacrylate] (PDMAEMA), was grafted onto the surface of cellulose nanocrystals via free radical polymerization. The resultant suspension of PDMAEMA-grafted-cellulose nanocrystals (PDMAEMA-g-CNC) possessed pH-responsive properties. The grafting was confirmed by FTIR, potentiometric titration, elementary analysis, and thermogravimetric analysis (TGA); the surface and interfacial properties of the modified particles were characterized by surface tensiometer. Compared to pristine cellulose nanocrystals, modified CNC significantly reduced the surface and interfacial tensions. Stable heptane-in-water and toluene-in-water emulsions were prepared with PDMAEMA-g-CNC. Various factors, such as polarity of solvents, concentration of particles, electrolytes, and pH, on the properties of the emulsions were investigated. Using Nile Red as a florescence probe, the stability of the emulsions as a function of pH and temperature was elucidated. It was deduced that PDMAEMA chains promoted the stability of emulsion droplets and their chain conformation varied with pH and temperature to trigger the emulsification and demulsification of oil droplets. Interestingly, for heptane system, the macroscopic colors varied depending on the pH condition, while the color of the toluene system remained the same. Reversible emulsion systems that responded to pH were observed and a thermoresponsive Pickering emulsion system was demonstrated.
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Stoichiometry and turnover of the bacterial flagellar switch protein FliN.
MBio
PUBLISHED: 07-03-2014
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Some proteins in biological complexes exchange with pools of free proteins while the complex is functioning. Evidence is emerging that protein exchange can be part of an adaptive mechanism. The bacterial flagellar motor is one of the most complex biological machines and is an ideal model system to study protein dynamics in large multimeric complexes. Recent studies showed that the copy number of FliM in the switch complex and the fraction of FliM that exchanges vary with the direction of flagellar rotation. Here, we investigated the stoichiometry and turnover of another switch complex component, FliN, labeled with the fluorescent protein CyPet, in Escherichia coli. Our results confirm that, in vivo, FliM and FliN form a complex with stoichiometry of 1:4 and function as a unit. We estimated that wild-type motors contained 120 ± 26 FliN molecules. Motors that rotated only clockwise (CW) or counterclockwise (CCW) contained 114 ± 17 and 144 ± 26 FliN molecules, respectively. The ratio of CCW-to-CW FliN copy numbers was 1.26, very close to that of 1.29 reported previously for FliM. We also measured the exchange of FliN molecules, which had a time scale and dependence upon rotation direction similar to those of FliM, consistent with an exchange of FliM-FliN as a unit. Our work confirms the highly dynamic nature of multimeric protein complexes and indicates that, under physiological conditions, these machines might not be the stable, complete structures suggested by averaged fixed methodologies but, rather, incomplete rings that can respond and adapt to changing environments. Importance: The flagellum is one of the most complex structures in a bacterial cell, with the core motor proteins conserved across species. Evidence is now emerging that turnover of some of these motor proteins depends on motor activity, suggesting that turnover is important for function. The switch complex transmits the chemosensory signal to the rotor, and we show, by using single-cell measurement, that both the copy number and the fraction of exchanging molecules vary with the rotational bias of the rotor. When the motor is locked in counterclockwise rotation, the copy number is similar to that determined by averaged, fixed methodologies, but when locked in a clockwise direction, the number is much lower, suggesting that that the switch complex ring is incomplete. Our results suggest that motor remodeling is an important component in tuning responses and adaptation at the motor.
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The structure of the cytomegalovirus-encoded m04 glycoprotein, a prototypical member of the m02 family of immunoevasins.
J. Biol. Chem.
PUBLISHED: 06-30-2014
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The ability of CMVs to evade the immune system of the host is dependent on the expression of a wide array of glycoproteins, many of which interfere with natural killer cell function. In murine CMV, two large protein families mediate this immune-evasive function. Although it is established that the m145 family members mimic the structure of MHC-I molecules, the structure of the m02 family remains unknown. The most extensively studied m02 family member is m04, a glycoprotein that escorts newly assembled MHC-I molecules to the cell surface, presumably to avoid "missing self" recognition. Here we report the crystal structure of the m04 ectodomain, thereby providing insight into this large immunoevasin family. m04 adopted a ?-sandwich immunoglobulin variable (Ig-V)-like fold, despite sharing very little sequence identity with the Ig-V superfamily. In addition to the Ig-V core, m04 possesses several unique structural features that included an unusual ?-strand topology, a number of extended loops and a prominent ?-helix. The m04 interior was packed by a myriad of hydrophobic residues that form distinct clusters around two conserved tryptophan residues. This hydrophobic core was well conserved throughout the m02 family, thereby indicating that murine CMV encodes a number of Ig-V-like molecules. We show that m04 binds a range of MHC-I molecules with low affinity in a peptide-independent manner. Accordingly, the structure of m04, which represents the first example of an murine CMV encoded Ig-V fold, provides a basis for understanding the structure and function of this enigmatic and large family of immunoevasins.
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Detection of Upper Airway Status and Respiratory Events by a Current Generation Positive Airway Pressure Device.
Sleep
PUBLISHED: 04-29-2014
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To compare a positive airway pressure (PAP) device's detection of respiratory events and airway status during device-detected apneas with events scored on simultaneous polysomnography (PSG).
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Modified Cellulose Nanocrystal for Vitamin C Delivery.
AAPS PharmSciTech
PUBLISHED: 03-26-2014
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Cellulose nanocrystal grafted with chitosan oligosaccharide (CNC-CSOS) was used to encapsulate vitamin C and prepare CNCS/VC complexes using tripolyphosphte via ionic complexation. The stability of vitamin C and the antioxidant activity of the CNCS/VC complexes were elucidated. The formation of the complex was confirmed using DSC and UV-vis spectrophotometry, and TEM was used to study the morphology of the complexes. The encapsulation efficiency of vitamin C at pH 3 and 5 was 71.6%?±?6.8 and 91.0?±?1.0, respectively. Strong exothermic peaks observed in isothermal titration calorimetric (ITC) studies at pH 5 could be attributed to additional electrostatic interactions between CNC-CSOS and vitamin C at pH 5. The in vitro release of vitamin C from CNCS/VC complexes showed a sustained release of up to 20 days. The vitamin C released from CNCS/VC complex displayed higher stability compared with the control vitamin C solution, and this was also confirmed from the ITC thermograms. CNC-CSOS possessed a higher scavenging activity and faster antioxidant activity compared with its precursors, i.e., oxidized CNC and CSOS and their physical mixtures. Complexing vitamin C into CNC-CSOS particles yielded a dynamic antioxidant agent, where the vitamin C is released over time and displayed sustained antioxidant properties. Therefore, CNCS/VC can potentially be used in cosmeceutical applications as topical formulations.
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Comparative release studies of two cationic model drugs from different cellulose nanocrystal derivatives.
Eur J Pharm Biopharm
PUBLISHED: 03-03-2014
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Native cellulose nanocrystal (CNC), oxidized CNC (CNC-OX) and chitosan oligosaccharide grafted CNC (CNC-CSOS) were evaluated as potential drug delivery carriers for two model drug compounds, procaine hydrochloride (PrHy) and imipramine hydrochloride (IMI). The loading of PrHy and IMI was performed at pH 8 and 7, respectively. IMI displayed higher binding to CNC derivatives than PrHy. Drug selective membranes were prepared for each model drug and a drug selective electrode system was used to measure the drug concentration in the filtrate and release medium. Isothermal Titration Calorimetry (ITC) was used to elucidate the types of interactions between model drugs and CNC and its derivatives. The complexation between model drugs and CNC derivatives was confirmed by zeta potential and transmittance measurements. The binding and release of these drugs correlated with the nature and types of interactions that exist between the CNC and drug molecules.
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Hybrid-fuel bacterial flagellar motors in Escherichia coli.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 02-18-2014
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The bacterial flagellar motor rotates driven by an electrochemical ion gradient across the cytoplasmic membrane, either H(+) or Na(+) ions. The motor consists of a rotor ?50 nm in diameter surrounded by multiple torque-generating ion-conducting stator units. Stator units exchange spontaneously between the motor and a pool in the cytoplasmic membrane on a timescale of minutes, and their stability in the motor is dependent upon the ion gradient. We report a genetically engineered hybrid-fuel flagellar motor in Escherichia coli that contains both H(+)- and Na(+)-driven stator components and runs on both types of ion gradient. We controlled the number of each type of stator unit in the motor by protein expression levels and Na(+) concentration ([Na(+)]), using speed changes of single motors driving 1-?m polystyrene beads to determine stator unit numbers. De-energized motors changed from locked to freely rotating on a timescale similar to that of spontaneous stator unit exchange. Hybrid motor speed is simply the sum of speeds attributable to individual stator units of each type. With Na(+) and H(+) stator components expressed at high and medium levels, respectively, Na(+) stator units dominate at high [Na(+)] and are replaced by H(+) units when Na(+) is removed. Thus, competition between stator units for spaces in a motor and sensitivity of each type to its own ion gradient combine to allow hybrid motors to adapt to the prevailing ion gradient. We speculate that a similar process may occur in species that naturally express both H(+) and Na(+) stator components sharing a common rotor.
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Structure of the chicken CD3??/? heterodimer and its assembly with the ??T cell receptor.
J. Biol. Chem.
PUBLISHED: 01-31-2014
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In mammals, the ??T cell receptor (TCR) signaling complex is composed of a TCR?? heterodimer that is noncovalently coupled to three dimeric signaling molecules, CD3??, CD3??, and CD3??. The nature of the TCR signaling complex and subunit arrangement in different species remains unclear however. Here we present a structural and biochemical analysis of the more primitive ancestral form of the TCR signaling complex found in chickens. In contrast to mammals, chickens do not express separate CD3? and CD3? chains but instead encode a single hybrid chain, termed CD3?/?, that is capable of pairing with CD3?. The NMR structure of the chicken CD3??/? heterodimer revealed a unique dimer interface that results in a heterodimer with considerable deviation from the distinct side-by-side architecture found in human and murine CD3?? and CD3??. The chicken CD3??/? heterodimer also contains a unique molecular surface, with the vast majority of surface-exposed, nonconserved residues being clustered to a single face of the heterodimer. Using an in vitro biochemical assay, we demonstrate that CD3??/? can assemble with both chicken TCR? and TCR? via conserved polar transmembrane sites. Moreover, analogous to the human TCR signaling complex, the presence of two copies of CD3??/? is required for ?? assembly. These data provide insight into the evolution of this critical receptor signaling apparatus.
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The Ly49 natural killer cell receptors: a versatile tool for viral self-discrimination.
Immunol. Cell Biol.
PUBLISHED: 01-14-2014
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The activation of murine and human natural killer (NK) cells is regulated by families of receptors including the Ly49 and Killer immunoglobulin-like receptors, respectively, both of which contain activating and inhibitory members. The archetypal role of inhibitory Ly49 receptors is to attenuate NK cell responses to normal cells that express major histocompatibility complex (MHC) class-I molecules, in essence allowing for more robust responses to infected or cancerous cells that lack MHC-I on their cell surface. However, it is now evident that Ly49 receptors have an appreciably more sophisticated array of functions. In particular, some activating Ly49 receptors can bind directly to MHC-I-like viral gene products such as m157, whereas others recognize self-MHC-I but only in the presence of viral chaperones. Although Ly49 receptor recognition is centred on the MHC-I-like fold, these NK cell receptors can also engage related ligands in unexpected ways. Herein we review the varied strategies employed by Ly49 receptors to recognize both self and viral ligands, with particular emphasis on the recently determined mode of Ly49-m157 ligation, and highlight the versatile nature of this family in the control of viral infections.
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Effective functional maturation of invariant natural killer T cells is constrained by negative selection and T-cell antigen receptor affinity.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 12-16-2013
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The self-reactivity of their T-cell antigen receptor (TCR) is thought to contribute to the development of immune regulatory cells, such as invariant NK T cells (iNKT). In the mouse, iNKT cells express TCRs composed of a unique V?14-J?18 rearrangement and recognize lipid antigens presented by CD1d molecules. We created mice expressing a transgenic TCR-? chain that confers high affinity for self-lipid/CD1d complexes when randomly paired with the mouse iNKT V?14-J?18 rearrangement to study their development. We show that although iNKT cells undergo agonist selection, their development is also shaped by negative selection in vivo. In addition, iNKT cells that avoid negative selection in these mice express natural sequence variants of the canonical TCR-? and decreased affinity for self/CD1d. However, limiting the affinity of the iNKT TCRs for "self" leads to inefficient Egr2 induction, poor expression of the iNKT lineage-specific zinc-finger transcription factor PLZF, inadequate proliferation of iNKT cell precursors, defects in trafficking, and impaired effector functions. Thus, proper development of fully functional iNKT cells is constrained by a limited range of TCR affinity that plays a key role in triggering the iNKT cell-differentiation pathway. These results provide a direct link between the affinity of the TCR expressed by T-cell precursors for self-antigens and the proper development of a unique population of lymphocytes essential to immune responses.
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Load-dependent assembly of the bacterial flagellar motor.
MBio
PUBLISHED: 08-22-2013
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It is becoming clear that the bacterial flagellar motor output is important not only for bacterial locomotion but also for mediating the transition from liquid to surface living. The output of the flagellar motor changes with the mechanical load placed on it by the external environment: at a higher load, the motor runs more slowly and produces higher torque. Here we show that the number of torque-generating units bound to the flagellar motor also depends on the external mechanical load, with fewer stators at lower loads. Stalled motors contained at least as many stators as rotating motors at high load, indicating that rotation is unnecessary for stator binding. Mutant stators incapable of generating torque could not be detected around the motor. We speculate that a component of the bacterial flagellar motor senses external load and mediates the strength of stator binding to the rest of the motor.
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Temperature dependences of torque generation and membrane voltage in the bacterial flagellar motor.
Biophys. J.
PUBLISHED: 08-07-2013
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In their natural habitats bacteria are frequently exposed to sudden changes in temperature that have been shown to affect their swimming. With our believed to be new methods of rapid temperature control for single-molecule microscopy, we measured here the thermal response of the Na(+)-driven chimeric motor expressed in Escherichia coli cells. Motor torque at low load (0.35 ?m bead) increased linearly with temperature, twofold between 15°C and 40°C, and torque at high load (1.0 ?m bead) was independent of temperature, as reported for the H(+)-driven motor. Single cell membrane voltages were measured by fluorescence imaging and these were almost constant (?120 mV) over the same temperature range. When the motor was heated above 40°C for 1-2 min the torque at high load dropped reversibly, recovering upon cooling below 40°C. This response was repeatable over as many as 10 heating cycles. Both increases and decreases in torque showed stepwise torque changes with unitary size ?150 pN nm, close to the torque of a single stator at room temperature (?180 pN nm), indicating that dynamic stator dissociation occurs at high temperature, with rebinding upon cooling. Our results suggest that the temperature-dependent assembly of stators is a general feature of flagellar motors.
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Mechanism and kinetics of a sodium-driven bacterial flagellar motor.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 06-20-2013
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The bacterial flagellar motor is a large rotary molecular machine that propels swimming bacteria, powered by a transmembrane electrochemical potential difference. It consists of an ?50-nm rotor and up to ?10 independent stators anchored to the cell wall. We measured torque-speed relationships of single-stator motors under 25 different combinations of electrical and chemical potential. All 25 torque-speed curves had the same concave-down shape as fully energized wild-type motors, and each stator passes at least 37 ± 2 ions per revolution. We used the results to explore the 25-dimensional parameter space of generalized kinetic models for the motor mechanism, finding 830 parameter sets consistent with the data. Analysis of these sets showed that the motor mechanism has a "powerstroke" in either ion binding or transit; ion transit is channel-like rather than carrier-like; and the rate-limiting step in the motor cycle is ion binding at low concentration, ion transit, or release at high concentration.
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Targeting of a natural killer cell receptor family by a viral immunoevasin.
Nat. Immunol.
PUBLISHED: 03-14-2013
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Activating and inhibitory receptors on natural killer (NK) cells have a crucial role in innate immunity, although the basis of the engagement of activating NK cell receptors is unclear. The activating receptor Ly49H confers resistance to infection with murine cytomegalovirus by binding to the immunoevasin m157. We found that m157 bound to the helical stalk of Ly49H, whereby two m157 monomers engaged the Ly49H dimer. The helical stalks of Ly49H lay centrally across the m157 platform, whereas its lectin domain was not required for recognition. Instead, m157 targeted an aromatic peg motif present in stalks of both activating and inhibitory receptors of the Ly49 family, and substitution of this motif abrogated binding. Furthermore, ligation of m157 to Ly49H or Ly49C resulted in intracellular signaling. Accordingly, m157 has evolved to tackle the legs of a family of NK cell receptors.
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Long-term use of a nasal expiratory positive airway pressure (EPAP) device as a treatment for obstructive sleep apnea (OSA).
J Clin Sleep Med
PUBLISHED: 10-18-2011
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Evaluate the long-term durability of treatment response and safety of a nasal expiratory positive airway pressure (EPAP) device used to treat obstructive sleep apnea (OSA).
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Collagen VI, conformation of A-domain arrays and microfibril architecture.
J. Biol. Chem.
PUBLISHED: 09-09-2011
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Collagen VI is a ubiquitous extracellular matrix protein that assembles into beaded microfibrils that form networks linking cells to the matrix. Collagen VI microfibrils are typically formed from a heterotrimer of the ?1, ?2, and ?3 chains. The ?3 chain is distinct as it contains an extended N terminus with up to 10 consecutive von Willebrand factor type A-domains (VWA). Here, we use solution small angle x-ray scattering (SAXS) and single particle analysis EM to determine the nanostructure of nine of these contiguous A-domains. Both techniques reveal a tight C-shape conformation for the A-domains. Furthermore, using biophysical approaches, we demonstrate that the N-terminal region undergoes a conformational change and a proportion forms dimers in the presence of Zn(2+). This is the first indication that divalent cations interact with collagen VI A-domains. A three-dimensional reconstruction of tissue-purified collagen VI microfibrils was generated using EM and single particle image analysis. The reconstruction showed the intricate architecture of the collagen VI globular regions, in particular the highly structurally conserved C-terminal region and variations in the appearance of the N-terminal region. The N-terminal domains project out from the globular beaded region like angled radial spokes. These could potentially provide interactive surfaces for other cell matrix molecules.
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Positive airway pressure initiation: a randomized controlled trial to assess the impact of therapy mode and titration process on efficacy, adherence, and outcomes.
Sleep
PUBLISHED: 08-02-2011
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(1) To determine the efficacy of automatically adjusted positive airway pressure (APAP) with a comfort feature (A-Flex) at reducing apneas and hypopneas in participants with moderate to severe OSA. (2) To determine the relative difference between A-Flex, continuous positive airway pressure (CPAP), and APAP-derived optimal pressure for CPAP (CPAP(APAP)) on adherence to treatment. (3) To determine the relative difference between APAP with A-Flex, CPAP, and CPAP(APAP) on long-term change in functional outcomes.
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Killer cell immunoglobulin-like receptor 3DL1-mediated recognition of human leukocyte antigen B.
Nature
PUBLISHED: 06-06-2011
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Members of the killer cell immunoglobulin-like receptor (KIR) family, a large group of polymorphic receptors expressed on natural killer (NK) cells, recognize particular peptide-laden human leukocyte antigen (pHLA) class I molecules and have a pivotal role in innate immune responses. Allelic variation and extensive polymorphism within the three-domain KIR family (KIR3D, domains D0-D1-D2) affects pHLA binding specificity and is linked to the control of viral replication and the treatment outcome of certain haematological malignancies. Here we describe the structure of a human KIR3DL1 receptor bound to HLA-B*5701 complexed with a self-peptide. KIR3DL1 clamped around the carboxy-terminal end of the HLA-B*5701 antigen-binding cleft, resulting in two discontinuous footprints on the pHLA. First, the D0 domain, a distinguishing feature of the KIR3D family, extended towards ?2-microglobulin and abutted a region of the HLA molecule with limited polymorphism, thereby acting as an innate HLA sensor domain. Second, whereas the D2-HLA-B*5701 interface exhibited a high degree of complementarity, the D1-pHLA-B*5701 contacts were suboptimal and accommodated a degree of sequence variation both within the peptide and the polymorphic region of the HLA molecule. Although the two-domain KIR (KIR2D) and KIR3DL1 docked similarly onto HLA-C and HLA-B respectively, the corresponding D1-mediated interactions differed markedly, thereby providing insight into the specificity of KIR3DL1 for discrete HLA-A and HLA-B allotypes. Collectively, in association with extensive mutagenesis studies at the KIR3DL1-pHLA-B*5701 interface, we provide a framework for understanding the intricate interplay between peptide variability, KIR3D and HLA polymorphism in determining the specificity requirements of this essential innate interaction that is conserved across primate species.
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Air leak is associated with poor adherence to autoPAP therapy.
Sleep
PUBLISHED: 06-02-2011
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To our knowledge, a systematic study of the effect of air leak on adherence to auto-titrating positive airway pressure (autoPAP) therapy has not been reported. We hypothesized that in patients with obstructive sleep apnea (OSA), greater levels of air leak were associated with poor adherence to autoPAP therapy.
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A novel nasal expiratory positive airway pressure (EPAP) device for the treatment of obstructive sleep apnea: a randomized controlled trial.
Sleep
PUBLISHED: 04-05-2011
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Investigate the efficacy of a novel nasal expiratory positive airway pressure (EPAP) device as a treatment for obstructive sleep apnea (OSA).
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Ocellar adaptations for dim light vision in a nocturnal bee.
J. Exp. Biol.
PUBLISHED: 03-25-2011
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Growing evidence indicates that insect ocelli are strongly adapted to meet the specific functional requirements in the environment in which that insect lives. We investigated how the ocelli of the nocturnal bee Megalopta genalis are adapted to life in the dim understory of a tropical rainforest. Using a combination of light microscopy and three-dimensional reconstruction, we found that the retinae contain bar-shaped rhabdoms loosely arranged in a radial pattern around multi-layered lenses, and that both lenses and retinae form complex non-spherical shapes reminiscent of those described in other ocelli. Intracellular electrophysiology revealed that the photoreceptors have high absolute sensitivity, but that the threshold location varied widely between 10(9) and 10(11) photons cm(-2) s(-1). Higher sensitivity and greater visual reliability may be obtained at the expense of temporal resolution: the corner frequencies of dark-adapted ocellar photoreceptors were just 4-11 Hz. Spectral sensitivity profiles consistently peaked at 500 nm. Unlike the ocelli of other flying insects, we did not detect UV-sensitive visual pigments in M. genalis, which may be attributable to a scarcity of UV photons under the rainforest canopy at night. In contrast to earlier predictions based on anatomy, the photoreceptors are not sensitive to the e-vector of polarised light. Megalopta genalis ocellar photoreceptors possess a number of unusual properties, including inherently high response variability and the ability to produce spike-like potentials. These properties bear similarities to photoreceptors in the compound eye of the cockroach, and we suggest that the two insects share physiological characteristics optimised for vision in dim light.
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Two methods of temperature control for single-molecule measurements.
Eur. Biophys. J.
PUBLISHED: 01-30-2011
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Modern single-molecule biophysical experiments require high numerical aperture oil-immersion objectives in close contact with the sample. We introduce two methods of high numerical aperture temperature control which can be implemented on any microscope: objective temperature control using a ring-shaped Peltier device, and stage temperature control using a fluid flow cooling chip in close thermal contact with the sample. We demonstrate the efficacy of each system by showing the change in speed with temperature of two molecular motors, the bacterial flagellar motor and skeletal muscle myosin.
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Insight into the basis of autonomous immunoreceptor activation.
Trends Immunol.
PUBLISHED: 01-25-2011
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Expression of the pre-T cell receptor (pTCR) by immature thymocytes is crucial for T cell development. The pTCR comprises an invariant pre-T? chain that pairs with a newly rearranged TCR? chain and CD3 signaling components. Despite its similarity to the mature ??TCR, which binds to specific peptide-loaded major histocompatibility molecules, the pTCR functions in a ligand-independent manner. Precisely how pTCR functions autonomously has remained a source of intense debate. Recently, the structure of the extracellular domain of the pTCR has been determined, providing insight into the mechanism of pTCR autonomous signaling. In this review, we reflect on the current understanding of pTCR function and draw comparisons to the mechanisms employed by the mature ??TCR and the related pre-B cell receptor.
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Steps and bumps: precision extraction of discrete states of molecular machines.
Biophys. J.
PUBLISHED: 01-22-2011
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We report statistical time-series analysis tools providing improvements in the rapid, precision extraction of discrete state dynamics from time traces of experimental observations of molecular machines. By building physical knowledge and statistical innovations into analysis tools, we provide techniques for estimating discrete state transitions buried in highly correlated molecular noise. We demonstrate the effectiveness of our approach on simulated and real examples of steplike rotation of the bacterial flagellar motor and the F1-ATPase enzyme. We show that our method can clearly identify molecular steps, periodicities and cascaded processes that are too weak for existing algorithms to detect, and can do so much faster than existing algorithms. Our techniques represent a step in the direction toward automated analysis of high-sample-rate, molecular-machine dynamics. Modular, open-source software that implements these techniques is provided.
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Myxobacteria gliding motility requires cytoskeleton rotation powered by proton motive force.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 01-19-2011
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Myxococcus xanthus is a Gram-negative bacterium that glides over surfaces without the aid of flagella. Two motility systems are used for locomotion: social-motility, powered by the retraction of type IV pili, and adventurous (A)-motility, powered by unknown mechanism(s). We have shown that AgmU, an A-motility protein, is part of a multiprotein complex that spans the inner membrane and periplasm of M. xanthus. In this paper, we present evidence that periplasmic AgmU decorates a looped continuous helix that rotates clockwise as cells glide forward, reversing its rotation when cells reverse polarity. Inhibitor studies showed that the AgmU helix rotation is driven by proton motive force (PMF) and depends on actin-like MreB cytoskeletal filaments. The AgmU motility complex was found to interact with MotAB homologs. Our data are consistent with a mechanochemical model in which PMF-driven motors, similar to bacterial flagella stator complexes, run along an endless looped helical track, driving rotation of the track; deformation of the cell surface by the AgmU-associated proteins creates pressure waves in the slime, pushing cells forward.
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The role of L(u)ck in T cell triggering.
Sci Signal
PUBLISHED: 01-18-2011
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T cells use a highly complex signaling apparatus to discriminate between a diverse array of foreign antigens and a myriad of self molecules. The precise mechanism whereby signals are communicated from the antigen-binding T cell receptor to the intracellular signal transduction machinery remains a source of intense debate. This Journal Club article highlights recent research elucidating the role of the Src family kinase Lck in T cell triggering. Resting T cells contain a newly described form of preactivated Lck that is both necessary and sufficient for T cell activation but remains uncoupled from the T cell receptor in the absence of antigen. This research allows a reappraisal of the mechanisms underlying T cell triggering.
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A simple backscattering microscope for fast tracking of biological molecules.
Rev Sci Instrum
PUBLISHED: 12-08-2010
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Recent developments in techniques for observing single molecules under light microscopes have helped reveal the mechanisms by which molecular machines work. A wide range of markers can be used to detect molecules, from single fluorophores to micron sized markers, depending on the research interest. Here, we present a new and simple objective-type backscattering microscope to track gold nanoparticles with nanometer and microsecond resolution. The total noise of our system in a 55 kHz bandwidth is ~0.6 nm per axis, sufficient to measure molecular movement. We found our backscattering microscopy to be useful not only for in vitro but also for in vivo experiments because of lower background scattering from cells than in conventional dark-field microscopy. We demonstrate the application of this technique to measuring the motion of a biological rotary molecular motor, the bacterial flagellar motor, in live Escherichia coli cells.
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Controlling the reflection wavelength of iridescent solid films of nanocrystalline cellulose.
Biomacromolecules
PUBLISHED: 12-06-2010
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Nanocrystalline cellulose (NCC) self-assembles in suspension to form iridescent chiral nematic films upon drying that can reflect circularly polarized light at specific wavelengths. Ultrasound treatment has now been found to increase the chiral nematic pitch in suspension and red-shift the reflection wavelength of NCC films as the applied energy increases. Sonication and electrolyte addition combined allow the reflective properties of the film to be predictably tuned. The effects of sonicating an NCC suspension are cumulative and permanent. Suspensions sonicated with different energy inputs may be mixed to give an NCC film having a reflection band intermediate between those obtained from the individual suspensions. The data suggest that the ultrasound-induced red-shift is electrostatic in nature.
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Best clinical practices for the sleep center adjustment of noninvasive positive pressure ventilation (NPPV) in stable chronic alveolar hypoventilation syndromes.
J Clin Sleep Med
PUBLISHED: 10-21-2010
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Noninvasive positive pressure ventilation (NPPV) devices are used during sleep to treat patients with diurnal chronic alveolar hypoventilation (CAH). Bilevel positive airway pressure (BPAP) using a mask interface is the most commonly used method to provide ventilatory support in these patients. BPAP devices deliver separately adjustable inspiratory positive airway pressure (IPAP) and expiratory positive airway pressure (EPAP). The IPAP and EPAP levels are adjusted to maintain upper airway patency, and the pressure support (PS = IPAP-EPAP) augments ventilation. NPPV devices can be used in the spontaneous mode (the patient cycles the device from EPAP to IPAP), the spontaneous timed (ST) mode (a backup rate is available to deliver IPAP for the set inspiratory time if the patient does not trigger an IPAP/EPAP cycle within a set time window), and the timed (T) mode (inspiratory time and respiratory rate are fxed). During NPPV titration with polysomnography (PSG), the pressure settings, backup rate, and inspiratory time (if applicable) are adjusted to maintain upper airway patency and support ventilation. However, there are no widely available guidelines for the titration of NPPV in the sleep center. A NPPV Titration Task Force of the American Academy of Sleep Medicine reviewed the available literature and developed recommendations based on consensus and published evidence when available. The major recommendations derived by this consensus process are as follows: General Recommendations: 1. The indications, goals of treatment, and side effects of NPPV treatment should be discussed in detail with the patient prior to the NPPV titration study. 2. Careful mask fitting and a period of acclimatization to low pressure prior to the titration should be included as part of the NPPV protocol. 3. NPPV titration with PSG is the recommended method to determine an effective level of nocturnal ventilatory support in patients with CAH. In circumstances in which NPPV treatment is initiated and adjusted empirically in the outpatient setting based on clinical judgment, a PSG should be utilized if possible to confirm that the final NPPV settings are effective or to make adjustments as necessary. 4. NPPV treatment goals should be individualized but typically include prevention of worsening of hypoventilation during sleep, improvement in sleep quality, relief of nocturnal dyspnea, and providing respiratory muscle rest. 5. When OSA coexists with CAH, pressure settings for treatment of OSA may be determined during attended NPPV titration PSG following AASM Clinical Guidelines for the Manual Titration of Positive Airway Pressure in Patients with Obstructive Sleep Apnea. 6. Attended NPPV titration with PSG is the recommended method to identify optimal treatment pressure settings for patients with the obesity hypoventilation syndrome (OHS), CAH due to restrictive chest wall disease (RTCD), and acquired or central CAH syndromes in whom NPPV treatment is indicated. 7. Attended NPPV titration with PSG allows definitive identification of an adequate level of ventilatory support for patients with neuromuscular disease (NMD) in whom NPPV treatment is planned. Recommendations for NPPV Titration Equipment: 1. The NPPV device used for titration should have the capability of operating in the spontaneous, spontaneous timed, and timed mode. 2. The airflow, tidal volume, leak, and delivered pressure signals from the NPPV device should be monitored and recorded if possible. The airflow signal should be used to detect apnea and hypopnea, while the tidal volume signal and respiratory rate are used to assess ventilation. 3. Transcutaneous or end-tidal PCO2 may be used to adjust NPPV settings if adequately calibrated and ideally validated with arterial blood gas testing. 4. An adequate assortment of masks (nasal, oral, and oronasal) in both adult and pediatric sizes (if children are being titrated), a source of supplemental oxygen, and heated humidification should be available. Recommendations for Limits of IPAP, EPAP, and PS Settings: 1. The recommended minimum starting IPAP and EPAP should be 8 cm H2O and 4 cm H2O, respectively. 2. The recommended maximum IPAP should be 30 cm H2O for patients > or = 12 years and 20 cm H2O for patients < 12 years. 3. The recommended minimum and maximum levels of PS are 4 cm H2O and 20 cm H2O, respectively. 4. The minimum and maximum incremental changes in PS should be 1 and 2 cm H2O, respectively. Recommendations for Adjustment of IPAP, EPAP, and PS: 1. IPAP and/or EPAP should be increased as described in AASM Clinical Guidelines for the Manual Titration of Positive Airway Pressure in Patients with Obstructive Sleep Apnea until the following obstructive respiratory events are eliminated (no specific order): apneas, hypopneas, respiratory effort-related arousals, and snoring. 2. The pressure support (PS) should be increased every 5 minutes if the tidal volume is low (< 6 to 8 mL/kg) 3. The PS should be increased if the arterial PCO2 remains 10 mm Hg or more above the PCO, goal at the current settings for 10 minutes or more. An acceptable goal for PCO, is a value less than or equal to the awake PCO2. 4. The PS may be increased if respiratory muscle rest has not been achieved by NPPV treatment at the current settings for 10 minutes of more. 5. The PS may be increased if the SpO, remains below 90% for 5 minutes or more and tidal volume is low (< 6 to 8 mL/kg). Recommendations for Use and Adjustment of the Backup Rate/ Respiratory Rate: 1. A backup rate (i.e., ST mode) should be used in all patients with central hypoventilation, those with a significant number of central apneas or an inappropriately low respiratory rate, and those who unreliably trigger IPAP/EPAP cycles due to muscle weakness. 2. The ST mode may be used if adequate ventilation or adequate respiratory muscle rest is not achieved with the maximum (or maximum tolerated) PS in the spontaneous mode. 3. The starting backup rate should be equal to or slightly less than the spontaneous sleeping respiratory rate (minimum of 10 bpm). 4. The backup rate should be increased in 1 to 2 bpm increments every 10 minutes if the desired goal of the backup rate has not been attained. 5. The IPAP time (inspiratory time) should be set based on the respiratory rate to provide an inspiratory time (IPAP time) between 30% and 40% of the cycle time (60/respiratory rate in breaths per minute). 6. If the spontaneous timed mode is not successful at meeting titration goals then the timed mode can be tried. Recommendations Concerning Supplemental Oxygen: 1. Supplemental oxygen may be added in patients with an awake SpO2 < 88% or when the PS and respiratory rate have been optimized but the SpO2 remains < 90% for 5 minutes or more. 2. The minimum starting supplemental oxygen rate should be 1 L/minute and increased in increments of 1 L/minute about every 5 minutes until an adequate SpO2 is attained (> 90%). Recommendations to Improve Patient Comfort and Patient-NPPV Device Synchrony: 1. If the patient awakens and complains that the IPAP and/or EPAP is too high, pressure should be lowered to a level comfortable enough to allow return to sleep. 2. NPPV device parameters (when available) such as pressure relief, rise time, maximum and minimum IPAP durations should be adjusted for patient comfort and to optimize synchrony between the patient and the NPPV device. 3. During the NPPV titration mask refit, adjustment, or change in mask type should be performed whenever any significant unintentional leak is observed or the patient complains of mask discomfort. If mouth leak is present and is causing significant symptoms (e.g., arousals) use of an oronasal mask or chin strap may be tried. Heated humidification should be added if the patient complains of dryness or significant nasal congestion. Recommendations for Follow-Up: 1. Close follow-up after initiation of NPPV by appropriately trained health care providers is indicated to establish effective utilization patterns, remediate side effects, and assess measures of ventilation and oxygenation to determine if adjustment to NPPV is indicated.
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Order within disorder: aggrecan chondroitin sulphate-attachment region provides new structural insights into protein sequences classified as disordered.
Proteins
PUBLISHED: 09-01-2010
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Structural investigation of proteins containing large stretches of sequences without predicted secondary structure is the focus of much increased attention. Here, we have produced an unglycosylated 30 kDa peptide from the chondroitin sulphate (CS)-attachment region of human aggrecan (CS-peptide), which was predicted to be intrinsically disordered and compared its structure with the adjacent aggrecan G3 domain. Biophysical analyses, including analytical ultracentrifugation, light scattering, and circular dichroism showed that the CS-peptide had an elongated and stiffened conformation in contrast to the globular G3 domain. The results suggested that it contained significant secondary structure, which was sensitive to urea, and we propose that the CS-peptide forms an elongated wormlike molecule based on a dynamic range of energetically equivalent secondary structures stabilized by hydrogen bonds. The dimensions of the structure predicted from small-angle X-ray scattering analysis were compatible with EM images of fully glycosylated aggrecan and a partly glycosylated aggrecan CS2-G3 construct. The semiordered structure identified in CS-peptide was not predicted by common structural algorithms and identified a potentially distinct class of semiordered structure within sequences currently identified as disordered. Sequence comparisons suggested some evidence for comparable structures in proteins encoded by other genes (PRG4, MUC5B, and CBP). The function of these semiordered sequences may serve to spatially position attached folded modules and/or to present polypeptides for modification, such as glycosylation, and to provide templates for the multiple pleiotropic interactions proposed for disordered proteins.
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Signal-dependent turnover of the bacterial flagellar switch protein FliM.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 05-24-2010
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Most biological processes are performed by multiprotein complexes. Traditionally described as static entities, evidence is now emerging that their components can be highly dynamic, exchanging constantly with cellular pools. The bacterial flagellar motor contains approximately 13 different proteins and provides an ideal system to study functional molecular complexes. It is powered by transmembrane ion flux through a ring of stator complexes that push on a central rotor. The Escherichia coli motor switches direction stochastically in response to binding of the response regulator CheY to the rotor switch component FliM. Much is known of the static motor structure, but we are just beginning to understand the dynamics of its individual components. Here we measure the stoichiometry and turnover of FliM in functioning flagellar motors, by using high-resolution fluorescence microscopy of E. coli expressing genomically encoded YPet derivatives of FliM at physiological levels. We show that the approximately 30 FliM molecules per motor exist in two discrete populations, one tightly associated with the motor and the other undergoing stochastic turnover. This turnover of FliM molecules depends on the presence of active CheY, suggesting a potential role in the process of motor switching. In many ways the bacterial flagellar motor is as an archetype macromolecular assembly, and our results may have further implications for the functional relevance of protein turnover in other large molecular complexes.
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The structural basis for autonomous dimerization of the pre-T-cell antigen receptor.
Nature
PUBLISHED: 04-20-2010
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The pre-T-cell antigen receptor (pre-TCR), expressed by immature thymocytes, has a pivotal role in early T-cell development, including TCR ?-selection, survival and proliferation of CD4(-)CD8(-) double-negative thymocytes, and subsequent ?? T-cell lineage differentiation. Whereas ??TCR ligation by the peptide-loaded major histocompatibility complex initiates T-cell signalling, pre-TCR-induced signalling occurs by means of a ligand-independent dimerization event. The pre-TCR comprises an invariant ?-chain (pre-T?) that pairs with any TCR ?-chain (TCR?) following successful TCR ?-gene rearrangement. Here we provide the basis of pre-T?-TCR? assembly and pre-TCR dimerization. The pre-T? chain comprised a single immunoglobulin-like domain that is structurally distinct from the constant (C) domain of the TCR ?-chain; nevertheless, the mode of association between pre-T? and TCR? mirrored that mediated by the C?-C? domains of the ??TCR. The pre-TCR had a propensity to dimerize in solution, and the molecular envelope of the pre-TCR dimer correlated well with the observed head-to-tail pre-TCR dimer. This mode of pre-TCR dimerization enabled the pre-T? domain to interact with the variable (V) ? domain through residues that are highly conserved across the V? and joining (J) ? gene families, thus mimicking the interactions at the core of the ??TCRs V?-V? interface. Disruption of this pre-T?-V? dimer interface abrogated pre-TCR dimerization in solution and impaired pre-TCR expression on the cell surface. Accordingly, we provide a mechanism of pre-TCR self-association that allows the pre-T? chain to simultaneously sample the correct folding of both the V and C domains of any TCR ?-chain, regardless of its ultimate specificity, which represents a critical checkpoint in T-cell development. This unusual dual-chaperone-like sensing function of pre-T? represents a unique mechanism in nature whereby developmental quality control regulates the expression and signalling of an integral membrane receptor complex.
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Time for bacteria to slow down.
Cell
PUBLISHED: 04-08-2010
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The speed of the bacterial flagellar motor is thought to be regulated by structural changes in the motor. Two new studies, Boehm et al. (2010) in this issue and Paul et al. (2010) in Molecular Cell, now show that cyclic di-GMP also regulates flagellar motor speed through interactions between the cyclic di-GMP binding protein YcgR and the motor proteins.
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A three-dimensional atlas of the honeybee neck.
PLoS ONE
PUBLISHED: 02-09-2010
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Three-dimensional digital atlases are rapidly becoming indispensible in modern biology. We used serial sectioning combined with manual registration and segmentation of images to develop a comprehensive and detailed three-dimensional atlas of the honeybee head-neck system. This interactive atlas includes skeletal structures of the head and prothorax, the neck musculature, and the nervous system. The scope and resolution of the model exceeds atlases previously developed on similar sized animals, and the interactive nature of the model provides a far more accessible means of interpreting and comprehending insect anatomy and neuroanatomy.
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Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch.
Science
PUBLISHED: 02-06-2010
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The bacterial flagellar switch that controls the direction of flagellar rotation during chemotaxis has a highly cooperative response. This has previously been understood in terms of the classic two-state, concerted model of allosteric regulation. Here, we used high-resolution optical microscopy to observe switching of single motors and uncover the stochastic multistate nature of the switch. Our observations are in detailed quantitative agreement with a recent general model of allosteric cooperativity that exhibits conformational spread--the stochastic growth and shrinkage of domains of adjacent subunits sharing a particular conformational state. We expect that conformational spread will be important in explaining cooperativity in other large signaling complexes.
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Uterine synechiae after bipolar hysteroscopic resection of submucosal myomas in patients with infertility.
Fertil. Steril.
PUBLISHED: 12-16-2009
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To determine the rate of uterine synechiae after bipolar hysteroscopic myomectomy in patients suffering from infertility.
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Structural and functional evidence for a substrate exclusion mechanism in mammalian tolloid like-1 (TLL-1) proteinase.
FEBS Lett.
PUBLISHED: 10-01-2009
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Bone morphogenetic protein-1 (BMP-1)/tolloid proteinases are fundamental to regulating dorsal ventral patterning and extracellular matrix deposition. In mammals there are four proteinases, the splice variants BMP-1 and mammalian tolloid (mTLD), and tolloid like-1 and -2 (TLL-1/2). BMP-1 has the highest catalytic activity and lacks three non-catalytic domains. We demonstrate that TLL-1, which has intermediate activity, forms a calcium-ion dependent dimer with monomers stacked side-by-side. In contrast, truncated TLL-1 molecules having the same shorter structure as BMP-1 are monomers and have improved activity towards their substrate chordin. The increased activity exceeds not only that of full-length TLL-1 but also BMP-1.
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A molecular brake, not a clutch, stops the Rhodobacter sphaeroides flagellar motor.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 07-01-2009
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Many bacterial species swim by employing ion-driven molecular motors that power the rotation of helical filaments. Signals are transmitted to the motor from the external environment via the chemotaxis pathway. In bidirectional motors, the binding of phosphorylated CheY (CheY-P) to the motor is presumed to instigate conformational changes that result in a different rotor-stator interface, resulting in rotation in the alternative direction. Controlling when this switch occurs enables bacteria to accumulate in areas favorable for their survival. Unlike most species that swim with bidirectional motors, Rhodobacter sphaeroides employs a single stop-start flagellar motor. Here, we asked, how does the binding of CheY-P stop the motor in R. sphaeroides--using a clutch or a brake? By applying external force with viscous flow or optical tweezers, we show that the R. sphaeroides motor is stopped using a brake. The motor stops at 27-28 discrete angles, locked in place by a relatively high torque, approximately 2-3 times its stall torque.
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Evaluation of hypoventilation.
Semin Respir Crit Care Med
PUBLISHED: 05-18-2009
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Evaluation of a patient with hypoventilation requires a combination of clinical history, physical examination, pulmonary function testing, and chest radiography to help determine the cause. Specialized testing such as measurement of respiratory muscle strength and assessment of ventilatory control may also be needed. Genetic testing may help make the diagnosis of some disorders such as the central congenital hypoventilation syndrome. In some patients the first laboratory clue that chronic hypoventilation is present is to note an unexplained elevation in the serum CO (2) (HCO (3)) on routine electrolyte testing. Nocturnal oximetry and polysomnography are usually required to determine if obstructive or central sleep apnea is present in addition to nocturnal hypoventilation. In addition, the severity of daytime hypoventilation or pulmonary function impairment often does not accurately predict the severity of nocturnal changes in arterial oxygen saturation and the degree of nocturnal hypoventilation. End-tidal PCO (2) and transcutaneous PCO (2) are sometimes utilized to directly estimate the degree of nocturnal hypoventilation during sleep studies. They have limitations but may be especially useful to detect trends in the PCO (2) during the night.
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Role of dimerization and substrate exclusion in the regulation of bone morphogenetic protein-1 and mammalian tolloid.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 05-08-2009
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The bone morphogenetic protein (BMP)-1/tolloid metalloproteinases are evolutionarily conserved enzymes that are fundamental to dorsal-ventral patterning and tissue morphogenesis. The lack of knowledge regarding how these proteinases recognize and cleave their substrates represents a major hurdle to understanding tissue assembly and embryonic patterning. Although BMP-1 and mammalian tolloid (mTLD) are splice variants, it is puzzling why BMP-1, which lacks 3 of the 7 noncatalytic domains present in all other family members, is the most effective proteinase. Using a combination of single-particle electron microscopy, small-angle X-ray scattering, and other biophysical measurements in solution, we show that mTLD, but not BMP-1, forms a calcium-ion-dependent dimer under physiological conditions. Using a domain deletion approach, we provide evidence that EGF2, which is absent in BMP-1, is critical to the formation of the dimer. Based on a combination of structural and functional data, we propose that mTLD activity is regulated by a substrate exclusion mechanism. These results provide a mechanistic insight into how alternative splicing of the Bmp1 gene produces 2 proteinases with differing biological activities and have broad implications for regulation of BMP-1/mTLD and related proteinases during BMP signaling and tissue assembly.
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Model studies of the dynamics of bacterial flagellar motors.
Biophys. J.
PUBLISHED: 01-14-2009
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The bacterial flagellar motor is a rotary molecular machine that rotates the helical filaments that propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation, and switching mechanism of the motor. In a previous article, we explained the general physics underneath the observed torque-speed curves with a simple two-state Fokker-Planck model. Here, we further analyze that model, showing that 1), the model predicts that the two components of the ion motive force can affect the motor dynamics differently, in agreement with latest experiments; 2), with explicit consideration of the stator spring, the model also explains the lack of dependence of the zero-load speed on stator number in the proton motor, as recently observed; and 3), the model reproduces the stepping behavior of the motor even with the existence of the stator springs and predicts the dwell-time distribution. The predicted stepping behavior of motors with two stators is discussed, and we suggest future experimental procedures for verification.
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High-resolution single-molecule characterization of the enzymatic states in Escherichia coli F1-ATPase.
Philos. Trans. R. Soc. Lond., B, Biol. Sci.
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The rotary motor F(1)-ATPase from the thermophilic Bacillus PS3 (TF(1)) is one of the best-studied of all molecular machines. F(1)-ATPase is the part of the enzyme F(1)F(O)-ATP synthase that is responsible for generating most of the ATP in living cells. Single-molecule experiments have provided a detailed understanding of how ATP hydrolysis and synthesis are coupled to internal rotation within the motor. In this work, we present evidence that mesophilic F(1)-ATPase from Escherichia coli (EF(1)) is governed by the same mechanism as TF(1) under laboratory conditions. Using optical microscopy to measure rotation of a variety of marker particles attached to the ?-subunit of single surface-bound EF(1) molecules, we characterized the ATP-binding, catalytic and inhibited states of EF(1). We also show that the ATP-binding and catalytic states are separated by 35±3°. At room temperature, chemical processes occur faster in EF(1) than in TF(1), and we present a methodology to compensate for artefacts that occur when the enzymatic rates are comparable to the experimental temporal resolution. Furthermore, we show that the molecule-to-molecule variation observed at high ATP concentration in our single-molecule assays can be accounted for by variation in the orientation of the rotating markers.
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Quantification of flagellar motor stator dynamics through in vivo proton-motive force control.
Mol. Microbiol.
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The bacterial flagellar motor, one of the few rotary motors in nature, produces torque to drive the flagellar filament by ion translocation through membrane-bound stator complexes. We used the light-driven proton pump proteorhodopsin (pR) to control the proton-motive force (PMF) in vivo by illumination. pR excitation was shown to be sufficient to replace native PMF generation, and when excited in cells with intact native PMF generation systems increased motor speed beyond the physiological norm. We characterized the effects of rapid in vivo PMF changes on the flagellar motor. Transient PMF disruption events from loss of illumination caused motors to stop, with rapid recovery of their previous rotation rate after return of illumination. However, extended periods of PMF loss led to stepwise increases in rotation rate upon PMF return as stators returned to the motor. The rate constant for stator binding to a putative single binding site on the motor was calculated to be 0.06 s(-1). Using GFP-tagged MotB stator proteins, we found that transient PMF disruption leads to reversible stator diffusion away from the flagellar motor, showing that PMF presence is necessary for continued motor integrity, and calculated a stator dissociation rate of 0.038 s(-1).
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Recognition of the nonclassical MHC class I molecule H2-M3 by the receptor Ly49A regulates the licensing and activation of NK cells.
Nat. Immunol.
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The development and function of natural killer (NK) cells is regulated by the interaction of inhibitory receptors of the Ly49 family with distinct peptide-laden major histocompatibility complex (MHC) class I molecules, although whether the Ly49 family is able bind to other MHC class I-like molecules is unclear. Here we found that the prototypic inhibitory receptor Ly49A bound the highly conserved nonclassical MHC class I molecule H2-M3 with an affinity similar to its affinity for H-2D(d). The specific recognition of H2-M3 by Ly49A regulated the licensing of NK cells and mediated missing-self recognition of H2-M3-deficient bone marrow. Host peptide-H2-M3 was required for optimal NK cell activity against experimental metastases and carcinogenesis. Thus, nonclassical MHC class I molecules can act as cognate ligands for Ly49 molecules. Our results provide insight into the various mechanisms that lead to NK cell tolerance.
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Rules for scoring respiratory events in sleep: update of the 2007 AASM Manual for the Scoring of Sleep and Associated Events. Deliberations of the Sleep Apnea Definitions Task Force of the American Academy of Sleep Medicine.
J Clin Sleep Med
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The American Academy of Sleep Medicine (AASM) Sleep Apnea Definitions Task Force reviewed the current rules for scoring respiratory events in the 2007 AASM Manual for the Scoring and Sleep and Associated Events to determine if revision was indicated. The goals of the task force were (1) to clarify and simplify the current scoring rules, (2) to review evidence for new monitoring technologies relevant to the scoring rules, and (3) to strive for greater concordance between adult and pediatric rules. The task force reviewed the evidence cited by the AASM systematic review of the reliability and validity of scoring respiratory events published in 2007 and relevant studies that have appeared in the literature since that publication. Given the limitations of the published evidence, a consensus process was used to formulate the majority of the task force recommendations concerning revisions.The task force made recommendations concerning recommended and alternative sensors for the detection of apnea and hypopnea to be used during diagnostic and positive airway pressure (PAP) titration polysomnography. An alternative sensor is used if the recommended sensor fails or the signal is inaccurate. The PAP device flow signal is the recommended sensor for the detection of apnea, hypopnea, and respiratory effort related arousals (RERAs) during PAP titration studies. Appropriate filter settings for recording (display) of the nasal pressure signal to facilitate visualization of inspiratory flattening are also specified. The respiratory inductance plethysmography (RIP) signals to be used as alternative sensors for apnea and hypopnea detection are specified. The task force reached consensus on use of the same sensors for adult and pediatric patients except for the following: (1) the end-tidal PCO(2) signal can be used as an alternative sensor for apnea detection in children only, and (2) polyvinylidene fluoride (PVDF) belts can be used to monitor respiratory effort (thoracoabdominal belts) and as an alternative sensor for detection of apnea and hypopnea (PVDFsum) only in adults.The task force recommends the following changes to the 2007 respiratory scoring rules. Apnea in adults is scored when there is a drop in the peak signal excursion by ? 90% of pre-event baseline using an oronasal thermal sensor (diagnostic study), PAP device flow (titration study), or an alternative apnea sensor, for ? 10 seconds. Hypopnea in adults is scored when the peak signal excursions drop by ? 30% of pre-event baseline using nasal pressure (diagnostic study), PAP device flow (titration study), or an alternative sensor, for ? 10 seconds in association with either ? 3% arterial oxygen desaturation or an arousal. Scoring a hypopnea as either obstructive or central is now listed as optional, and the recommended scoring rules are presented. In children an apnea is scored when peak signal excursions drop by ? 90% of pre-event baseline using an oronasal thermal sensor (diagnostic study), PAP device flow (titration study), or an alternative sensor; and the event meets duration and respiratory effort criteria for an obstructive, mixed, or central apnea. A central apnea is scored in children when the event meets criteria for an apnea, there is an absence of inspiratory effort throughout the event, and at least one of the following is met: (1) the event is ? 20 seconds in duration, (2) the event is associated with an arousal or ? 3% oxygen desaturation, (3) (infants under 1 year of age only) the event is associated with a decrease in heart rate to less than 50 beats per minute for at least 5 seconds or less than 60 beats per minute for 15 seconds. A hypopnea is scored in children when the peak signal excursions drop is ? 30% of pre-event baseline using nasal pressure (diagnostic study), PAP device flow (titration study), or an alternative sensor, for ? the duration of 2 breaths in association with either ? 3% oxygen desaturation or an arousal. In children and adults, surrogates of the arterial PCO(2) are the end-tidal PCO(2) or transcutaneous PCO(2) (diagnostic study) or transcutaneous PCO(2) (titration study). For adults, sleep hypoventilation is scored when the arterial PCO(2) (or surrogate) is > 55 mm Hg for ? 10 minutes or there is an increase in the arterial PCO(2) (or surrogate) ? 10 mm Hg (in comparison to an awake supine value) to a value exceeding 50 mm Hg for ? 10 minutes. For pediatric patients hypoventilation is scored when the arterial PCO(2) (or surrogate) is > 50 mm Hg for > 25% of total sleep time. In adults Cheyne-Stokes breathing is scored when both of the following are met: (1) there are episodes of ? 3 consecutive central apneas and/or central hypopneas separated by a crescendo and decrescendo change in breathing amplitude with a cycle length of at least 40 seconds (typically 45 to 90 seconds), and (2) there are five or more central apneas and/or central hypopneas per hour associated with the crescendo/decrescendo breathing pattern recorded over a minimum of 2 hours of monitoring.
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DEC-205 is a cell surface receptor for CpG oligonucleotides.
Proc. Natl. Acad. Sci. U.S.A.
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Synthetic CpG oligonucleotides (ODN) have potent immunostimulatory properties exploited in clinical vaccine trials. How CpG ODN are captured and delivered to the intracellular receptor TLR9, however, has been elusive. Here we show that DEC-205, a multilectin receptor expressed by a variety of cells, is a receptor for CpG ODN. When CpG ODN are used as an adjuvant, mice deficient in DEC-205 have impaired dendritic cell (DC) and B-cell maturation, are unable to make some cytokines such as IL-12, and display suboptimal cytotoxic T-cell responses. We reveal that DEC-205 directly binds class B CpG ODN and enhances their uptake. The CpG-ODN binding function of DEC-205 is conserved between mouse and man, although human DEC-205 preferentially binds a specific class B CpG ODN that has been selected for human clinical trials. Our findings identify an important receptor for class B CpG ODN and reveal a unique function for DEC-205.
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The Microbial Olympics.
Nat. Rev. Microbiol.
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Every four years, the Olympic Games plays host to competitors who have built on their natural talent by training for many years to become the best in their chosen discipline. Similar spirit and endeavour can be found throughout the microbial world, in which every day is a competition to survive and thrive. Microorganisms are trained through evolution to become the fittest and the best adapted to a particular environmental niche or lifestyle, and to innovate when the rules of the game are changed by alterations to their natural habitats. In this Essay, we honour the best competitors in the microbial world by inviting them to take part in the inaugural Microbial Olympics.
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Conformational spread in the flagellar motor switch: a model study.
PLoS Comput. Biol.
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The reliable response to weak biological signals requires that they be amplified with fidelity. In E. coli, the flagellar motors that control swimming can switch direction in response to very small changes in the concentration of the signaling protein CheY-P, but how this works is not well understood. A recently proposed allosteric model based on cooperative conformational spread in a ring of identical protomers seems promising as it is able to qualitatively reproduce switching, locked state behavior and Hill coefficient values measured for the rotary motor. In this paper we undertook a comprehensive simulation study to analyze the behavior of this model in detail and made predictions on three experimentally observable quantities: switch time distribution, locked state interval distribution, Hill coefficient of the switch response. We parameterized the model using experimental measurements, finding excellent agreement with published data on motor behavior. Analysis of the simulated switching dynamics revealed a mechanism for chemotactic ultrasensitivity, in which cooperativity is indispensable for realizing both coherent switching and effective amplification. These results showed how cells can combine elements of analog and digital control to produce switches that are simultaneously sensitive and reliable.
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Flagellar hook flexibility is essential for bundle formation in swimming Escherichia coli cells.
J. Bacteriol.
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Swimming Escherichia coli cells are propelled by the rotary motion of their flagellar filaments. In the normal swimming pattern, filaments positioned randomly over the cell form a bundle at the posterior pole. It has long been assumed that the hook functions as a universal joint, transmitting rotation on the motor axis through up to ?90° to the filament in the bundle. Structural models of the hook have revealed how its flexibility is expected to arise from dynamic changes in the distance between monomers in the helical lattice. In particular, each of the 11 protofilaments that comprise the hook is predicted to cycle between short and long forms, corresponding to the inside and outside of the curved hook, once each revolution of the motor when the hook is acting as a universal joint. To test this, we genetically modified the hook so that it could be stiffened by binding streptavidin to biotinylated monomers, impeding their motion relative to each other. We found that impeding the action of the universal joint resulted in atypical swimming behavior as a consequence of disrupted bundle formation, in agreement with the universal joint model.
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Dispersibility in water of dried nanocrystalline cellulose.
Biomacromolecules
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Dispersibility is important for nanocrystalline cellulose (NCC) because recovering the unique suspension and particle properties is essential after the product has been dried for storage or transport. It is our goal to produce dried NCC that redisperses in water to yield colloidal suspensions without the use of additives or a large energy input. In contrast with the as-prepared acidic form of NCC (H-NCC), suspensions of neutral sodium-form NCC (Na-NCC) dried by evaporation, lyophilization, or spray-drying are readily dispersible in water. Suspension properties and NCC particle size determined by light scattering were used as indicators of dispersion quality. The neutral counterion content, drying technique, freezing action, drying and redispersion concentrations, and moisture content in the dried NCC were all found to influence dispersibility. When a minimum of 94% of the H(+) counterion is exchanged for Na(+), the neutral salt form is fully dispersible in water even when fully dried. Mild sonication is generally sufficient to recover measured particle sizes identical to those in the never-dried Na-NCC sample. A threshold moisture content of 4 wt % was found, above which dried H-NCC is fully dispersible in water.
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Predictors of clinical pain in fibromyalgia: examining the role of sleep.
J Pain
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Understanding individual differences in the variability of fibromyalgia pain can help elucidate etiological mechanisms and treatment targets. Past research has shown that spatial extent of pain, negative mood, and aftersensation (pain ratings taken after experimental induction of pain) accounts for 40 to 50% of the variance in clinical pain. Poor sleep is hypothesized to have a reciprocal relationship with pain, and over 75% of individuals with fibromyalgia report disturbed sleep. We hypothesized that measures of sleep would increase the predictive ability of the clinical pain model. Measures of usual pain, spatial extent of pain, negative mood, and pain aftersensation were taken from 74 adults with fibromyalgia. Objective (actigraph) and subjective (diary) measures of sleep duration and nightly wake time were also obtained from the participants over 14 days. Hierarchical regression indicated that greater spatial extent (R(2) = .26), higher aftersensation ratings (R(2) = .06), and higher negative mood (R(2) = .04) accounted for 36% of the variance in clinical pain (average of 14 daily pain ratings). None of the sleep variables were significant predictors of clinical pain. Results replicate previous research and suggest that spatial extent of pain, pain aftersensation, and negative mood play important roles in clinical pain, but sleep disturbance did not aid in its prediction.
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Respiratory event detection by a positive airway pressure device.
Sleep
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Compare automatic event detection (AED) of respiratory events using a positive airway pressure (PAP) device with manual scoring of polysomnography (PSG) during PAP treatment of obstructive sleep apnea (OSA).
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.