This title is part of UC Press's Voices Revived program, which commemorates University of California Press's mission to seek out and cultivate the brightest minds and give them voice, reach, and ...impact. Drawing on a backlist dating to 1893, Voices Revived makes high-quality, peer-reviewed scholarship accessible once again using print-on-demand technology. This title was originally published in 1959.
Small-angle X-ray scattering (SAXS) is a powerful method to study the structural properties of materials at the nanoscale. Recent progress in instrumentation and analysis methods has led to rapidly ...growing applications of this technique for the characterization of biological macromolecules in solution. Ab initio and rigid-body modeling methods allow one to build three-dimensional, low-resolution models from SAXS data. With the new approaches, oligomeric states of proteins and macromolecular complexes can be assessed, chemical equilibria and kinetic reactions can be studied, and even flexible objects such as intrinsically unfolded proteins can be quantitatively characterized. This review describes the analysis methods of SAXS data from macromolecular solutions, ranging from the computation of overall structural parameters to advanced three-dimensional modeling. The efficiency of these methods is illustrated by recent applications to biological macromolecules and nanocomposite particles.
A high‐brilliance synchrotron P12 beamline of the EMBL located at the PETRA III storage ring (DESY, Hamburg) is dedicated to biological small‐angle X‐ray scattering (SAXS) and has been designed and ...optimized for scattering experiments on macromolecular solutions. Scatterless slits reduce the parasitic scattering, a custom‐designed miniature active beamstop ensures accurate data normalization and the photon‐counting PILATUS 2M detector enables the background‐free detection of weak scattering signals. The high flux and small beam size allow for rapid experiments with exposure time down to 30–50 ms covering the resolution range from about 300 to 0.5 nm. P12 possesses a versatile and flexible sample environment system that caters for the diverse experimental needs required to study macromolecular solutions. These include an in‐vacuum capillary mode for standard batch sample analyses with robotic sample delivery and for continuous‐flow in‐line sample purification and characterization, as well as an in‐air capillary time‐resolved stopped‐flow setup. A novel microfluidic centrifugal mixing device (SAXS disc) is developed for a high‐throughput screening mode using sub‐microlitre sample volumes. Automation is a key feature of P12; it is controlled by a beamline meta server, which coordinates and schedules experiments from either standard or nonstandard operational setups. The integrated SASFLOW pipeline automatically checks for consistency, and processes and analyses the data, providing near real‐time assessments of overall parameters and the generation of low‐resolution models within minutes of data collection. These advances, combined with a remote access option, allow for rapid high‐throughput analysis, as well as time‐resolved and screening experiments for novice and expert biological SAXS users.
Paraoxonase-1 (PON1), an esterase/lactonase primarily associated with plasma high-density lipoprotein (HDL), was the first member of this family of enzymes to be characterized. Its name was derived ...from its ability to hydrolyze paraoxon, the toxic metabolite of the insecticide parathion. Related enzymes PON2 and PON3 were named from their evolutionary relationship with PON1. Mice with each PON gene knocked out were generated at UCLA and have been key for elucidating their roles in organophosphorus (OP) metabolism, cardiovascular disease, innate immunity, obesity, and cancer. PON1 status, determined with two-substrate analyses, reveals an individual’s functional Q192R genotype and activity levels. The three-dimensional structure for a chimeric PON1 has been useful for understanding the structural properties of PON1 and for engineering PON1 as a catalytic scavenger of OP compounds. All three PONs hydrolyze microbial N-acyl homoserine lactone quorum sensing factors, quenching Pseudomonas aeruginosa’s pathogenesis. All three PONs modulate oxidative stress and inflammation. PON2 is localized in the mitochondria and endoplasmic reticulum. PON2 has potent antioxidant properties and is found at 3- to 4-fold higher levels in females than males, providing increased protection against oxidative stress, as observed in primary cultures of neurons and astrocytes from female mice compared with male mice. The higher levels of PON2 in females may explain the lower frequency of neurological and cardiovascular diseases in females and the ability to identify males but not females with Parkinson’s disease using a special PON1 status assay. Less is known about PON3; however, recent experiments with PON3 knockout mice show them to be susceptible to obesity, gallstone formation and atherosclerosis. Like PONs 1 and 2, PON3 also appears to modulate oxidative stress. It is localized in the endoplasmic reticulum, mitochondria and on HDL. Both PON2 and PON3 are upregulated in cancer, favoring tumor progression through mitochondrial protection against oxidative stress and apoptosis.
•Paraoxonases are lipo-lactonases with shared and unique substrate specificities.•PONs are associated with a variety of human diseases and PON1 with OP exposures.•PON1 activity measurement is important when assessing risk of exposure or disease.•Intracellular PON2 protects against oxidative stress and apoptosis.•PON3 seems to have similar functions and shares localization with PON1 and PON2.
Autoimmune thyroid disease (AITD) is the most prevalent autoimmune disease. It shares multiple genetic, clinical, and serologic characteristics with rheumatoid arthritis (RA). Although frequently ...described as a classic form of single-organ autoimmunity, the AITD disease burden in a subset of patients extends well beyond the thyroid gland. This review explores the complex interaction between the two diseases and the clinical consequences when they overlap. Beyond the well-known effects of AITD on thyroid function in RA, there is mounting evidence of the association of both conditions impacting the presentation and outcomes of diabetes, metabolic syndrome, and cardiovascular disease. An increasing number of studies suggest that there are negative effects of AITD on RA disease activity both in the presence and in the absence of thyroid dysfunction. Recent evidence suggests that AITD may not only worsen the cumulative damage of RA through higher disease activity but may also worsen secondary osteoarthritis changes. Less well-known is the significant association between AITD and chronic widespread pain syndromes including fibromyalgia. Importantly, the presence of fibromyalgia, which is increased in RA patients, appears to be further increased when it overlaps with AITD. Lastly, we probe the possible influence of AITD interacting with RA on fertility and clinical depression.
Key Points
• Autoimmune thyroid disease is the most common autoimmune disease and is frequently associated with rheumatoid arthritis.
• Autoimmune thyroid disease can present with osteoarthritis, inflammatory arthritis, and chronic widespread pain syndromes.
• The co-occurrence of autoimmune thyroid disease and rheumatoid arthritis may worsen disease activity and exacerbate other disease manifestations including cardiovascular disease, fertility, and depression.
• The overlap of rheumatoid arthritis with autoimmune thyroid disease needs further research and should be sought in general clinical practice.
Paraoxonase 1 (PON1) is a high density lipoprotein (HDL)-associated enzyme displaying esterase and lactonase activity. PON1 hydrolyzes several organophosphorus (OP) insecticides and nerve agents, a ...number of exogenous and endogenous lactones, and metabolizes toxic oxidized lipids of low density lipoproteins (LDL) and HDL. As such, PON1 plays a relevant role in determining susceptibility to OP toxicity, cardiovascular diseases and several other diseases. Serum PON1 activity in a given population can vary by at least 40-fold. Most of this variation can be accounted for by genetic polymorphisms in the coding region (Q192R, L55M) and in the promoter region (T-108C). However, exogenous factors may also modulate PON1 activity and/or level of expression. This paper examines various factors that have been found to positively modulate PON1. Certain drugs (e.g. hypolipemic and anti-diabetic compounds), dietary factors (antioxidants, polyphenols), and life-style factors (moderate alcohol consumption) appear to increase PON1 activity. Given the relevance of PON1 in protecting from certain environmental exposure and from cardiovascular and other diseases, there is a need for further mechanistic, animal, and clinical research in this area, and for consideration of possible alternative strategies for increasing the levels and activity of PON1.
The induced diffusion of tracers in a bacterial suspension is studied theoretically and experimentally at low bacterial concentrations. Considering the swimmer–tracer hydrodynamic interactions at low ...Reynolds number and using a kinetic theory approach, it is shown that the induced diffusion coefficient is proportional to the swimmer concentration, their mean velocity and a coefficient
$\beta $
, as observed experimentally. This paper shows that
$\beta $
increases as a result of the interaction with solid surfaces. The coefficient
$\beta $
scales as the tracer–swimmer cross-section times the mean square displacement produced by single scattering events, which depends on the swimmer propulsion forces. Considering simple swimmer models (acting on the fluid as two monopoles or as a force dipole), it is shown that
$\beta $
increases for decreasing swimming efficiencies. Close to solid surfaces, the swimming efficiency degrades and, consequently, the induced diffusion increases. Experiments on wild-type Escherichia coli in a Hele-Shaw cell, under buoyant conditions, are performed to measure the induced diffusion on tracers near surfaces. The modification of the suspension pH varies the swimmers’ velocity over a wide range, allowing the
$\beta $
coefficient to be extracted with precision. It is found that solid surfaces modify the induced diffusion: decreasing the confinement height of the cell,
$\beta $
increases by a factor of 4. The theoretical model reproduces this increase, although there are quantitative differences, probably attributed to the simplicity of the swimmer models and to the estimates for the parameters that model E. coli.
Small‐angle X‐ray scattering (SAXS) of macromolecules in solution is in increasing demand by an ever more diverse research community, both academic and industrial. To better serve user needs, and to ...allow automated and high‐throughput operation, a sample changer (BioSAXS Sample Changer) that is able to perform unattended measurements of up to several hundred samples per day has been developed. The Sample Changer is able to handle and expose sample volumes of down to 5 µl with a measurement/cleaning cycle of under 1 min. The samples are stored in standard 96‐well plates and the data are collected in a vacuum‐mounted capillary with automated positioning of the solution in the X‐ray beam. Fast and efficient capillary cleaning avoids cross‐contamination and ensures reproducibility of the measurements. Independent temperature control for the well storage and for the measurement capillary allows the samples to be kept cool while still collecting data at physiological temperatures. The Sample Changer has been installed at three major third‐generation synchrotrons: on the BM29 beamline at the European Synchrotron Radiation Facility (ESRF), the P12 beamline at the PETRA‐III synchrotron (EMBL@PETRA‐III) and the I22/B21 beamlines at Diamond Light Source, with the latter being the first commercial unit supplied by Bruker ASC.
We investigate experimentally the emergence of collective motion in the bulk of an active suspension of Escherichia coli bacteria. When increasing the concentration from a dilute to a semi-dilute ...regime, we observe a continuous crossover from a dynamical cluster regime to a regime of 'bio-turbulence' convection patterns. We measure a length scale characterizing the collective motion as a function of the bacteria concentration. For bacteria fully supplied with oxygen, the increase of the correlation length is almost linear with concentration and at the largest concentrations tested, the correlation length could be as large as 24 bacterial body sizes (or 7-8 when including the flagella bundle). In contrast, under conditions of oxygen shortage the correlation length saturates at a value of around 7 body lengths.
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