Stochastic chain termination in bacterial pilus assembly

Adhesive type 1 pili from uropathogenic Escherichia coli strains are filamentous, supramolecular protein complexes consisting of a short tip fibrillum and a long, helical rod formed by up to several thousand copies of the major pilus subunit FimA. Here, we reconstituted the entire type 1 pilus rod assembly reaction in vitro, using all constituent protein subunits in the presence of the assembly platform FimD, and identified the so-far uncharacterized subunit FimI as an irreversible assembly terminator. We provide a complete, quantitative model of pilus rod assembly kinetics based on the measured rate constants of FimD-catalyzed subunit incorporation. The model reliably predicts the length distribution of assembled pilus rods as a function of the ratio between FimI and the main pilus subunit FimA and is fully consistent with the length distribution of membrane-anchored pili assembled in vivo. The results show that the natural length distribution of adhesive pili formed via the chaperone-usher pathway results from a stochastic chain termination reaction. In addition, we demonstrate that FimI contributes to anchoring the pilus to the outer membrane and report the crystal structures of (i) FimI in complex with the assembly chaperone FimC, (ii) the FimI-FimC complex bound to the N-terminal domain of FimD, and (iii) a ternary complex between FimI, FimA and FimC that provides structural insights on pilus assembly termination and pilus anchoring by FimI.

Spectroscopic glimpses of the transition state of ATP hydrolysis trapped in a bacterial DnaB helicase

The ATP hydrolysis transition state of motor proteins is a weakly populated protein state that can be stabilized and investigated by replacing ATP with chemical mimics. We present atomic-level structural and dynamic insights on a state created by ADP aluminum fluoride binding to the bacterial DnaB helicase from Helicobacter pylori. We determined the positioning of the metal ion cofactor within the active site using electron paramagnetic resonance, and identified the protein protons coordinating to the phosphate groups of ADP and DNA using proton-detected 31P,1H solid-state nuclear magnetic resonance spectroscopy at fast magic-angle spinning > 100 kHz, as well as temperature-dependent proton chemical-shift values to prove their engagements in hydrogen bonds. 19F and 27Al MAS NMR spectra reveal a highly mobile, fast-rotating aluminum fluoride unit pointing to the capture of a late ATP hydrolysis transition state in which the phosphoryl unit is already detached from the arginine and lysine fingers.

Biomolecular solid-state NMR spectroscopy at 1200 MHz: the gain in resolution

Progress in NMR in general and in biomolecular applications in particular is driven by increasing magnetic-field strengths leading to improved resolution and sensitivity of the NMR spectra. Recently, persistent superconducting magnets at a magnetic field strength (magnetic induction) of 28.2 T corresponding to 1200 MHz proton resonance frequency became commercially available. We present here a collection of high-field NMR spectra of a variety of proteins, including molecular machines, membrane proteins, viral capsids, fibrils and large molecular assemblies. We show this large panel in order to provide an overview over a range of representative systems under study, rather than a single best performing model system. We discuss both carbon-13 and proton-detected experiments, and show that in ¹³C spectra substantially higher numbers of peaks can be resolved compared to 850 MHz while for ¹H spectra the most impressive increase in resolution is observed for aliphatic side-chain resonances.

Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications

The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.

Dimer Organization of Membrane-Associated NS5A of Hepatitis C Virus as Determined by Highly Sensitive 1 H-Detected Solid-State NMR

The Hepatitis C virus nonstructural protein 5A (NS5A) is a membrane-associated protein involved in multiple steps of the viral life cycle. Direct-acting antivirals (DAAs) targeting NS5A are a cornerstone of antiviral therapy, but the mode-of-action of these drugs is poorly understood. This is due to the lack of information on the membrane-bound NS5A structure. Herein, we present the structural model of an NS5A AH-linker-D1 protein reconstituted as proteoliposomes. We use highly sensitive proton-detected solid-state NMR methods suitable to study samples generated through synthetic biology approaches. Spectra analyses disclose that both the AH membrane anchor and the linker are highly flexible. Paramagnetic relaxation enhancements (PRE) reveal that the dimer organization in lipids requires a new type of NS5A self-interaction not reflected in previous crystal structures. In conclusion, we provide the first characterization of NS5A AH-linker-D1 in a lipidic environment shedding light onto the mode-of-action of clinically used NS5A inhibitors.

Comparison of the Efficacy and Safety of two Formulations of Diclofenac Sodium 0.1 % Eyedrops in Controlling Postoperative Inflammation after Cataract Surgery

PURPOSE

To compare the efficacy and safety of diclofenac sodium 0.1% eyedrops packaged in an Abak multidose container without preservative (Dicloabak) with the reference product, sodium merthiolate-preserved diclofenac sodium 0.1% eyedrops, in controlling postoperative inflammation after cataract surgery.

METHODS

The multicenter, controlled, randomized, single-masked study included 194 patients (Dicloabak 96, preserved diclofenac 98) scheduled to have cataract surgery by phacoemulsification with foldable intraocular lens. All were evaluated preoperatively and postoperatively after 1, 7, and 28 days. Postoperative inflammation was measured by the total score of anterior chamber cells and flare. Ocular plin, conjunctival hyperemia and ciliary flush were also assessed. Postoperative patient assessments also included visual acuity, objective tolerance by slit-lamp, fluorescein test, and subjective evaluation of local tolerance.

RESULTS

There was no statistically significant difference between the groups in the total score of flare and cells or the degree of conjunctival hyperemia and ciliary flush at any study visit. Dicloabak was demonstrated to be not inferior to preserved diclofenac at all assessment times. The overall assessment of local tolerance was similar for both study medications.

CONCLUSIONS

Preservative suppression did not alter diclofenac efficacy. Results support the good safety profile of both formulations when dosed three times daily for 4 weeks in absence of concomitant use of drugs potentially toxic for cornea. Preservative-free formulations like Dicloabak should be preferred to generic diclofenac formulations including other ingredients and may improve the safety profile of this topical nonsteroid anti-inflammatory drug.

Antarctic ice sheet discharge driven by atmosphere-ocean feedbacks at the Last Glacial Termination

Reconstructing the dynamic response of the Antarctic ice sheets to warming during the Last Glacial Termination (LGT; 18,000–11,650 yrs ago) allows us to disentangle ice-climate feedbacks that are key to improving future projections. Whilst the sequence of events during this period is reasonably well-known, relatively poor chronological control has precluded precise alignment of ice, atmospheric and marine records, making it difficult to assess relationships between Antarctic ice-sheet (AIS) dynamics, climate change and sea level. Here we present results from a highly-resolved ‘horizontal ice core’ from the Weddell Sea Embayment, which records millennial-scale AIS dynamics across this extensive region. Counterintuitively, we find AIS mass-loss across the full duration of the Antarctic Cold Reversal (ACR; 14,600–12,700 yrs ago), with stabilisation during the subsequent millennia of atmospheric warming. Earth-system and ice-sheet modelling suggests these contrasting trends were likely Antarctic-wide, sustained by feedbacks amplified by the delivery of Circumpolar Deep Water onto the continental shelf. Given the anti-phase relationship between inter-hemispheric climate trends across the LGT our findings demonstrate that Southern Ocean-AIS feedbacks were controlled by global atmospheric teleconnections. With increasing stratification of the Southern Ocean and intensification of mid-latitude westerly winds today, such teleconnections could amplify AIS mass loss and accelerate global sea-level rise.

Microgravity culture reduces apoptosis and increases the differentiation of a human colorectal carcinoma cell line

Our hypothesis is that rotation increases apoptosis in standard tissue culture medium at shear stresses of greater than approximately 0.3 dyn/cm2. Human MIP-101 poorly differentiated colorectal carcinoma cells were cultured for 6 d in complete medium in monolayers, on Teflon-coated nonadherent surfaces (static three-dimensional [3D]) or in rotating 3D cultures either in microgravity in low-earth orbit (3D microg) or in unit gravity on the ground (3D 1g). Apoptosis (determined morphologically), proliferation (by MIB1 staining), and the expression of epidermal growth-factor receptor (EGF-R), TGF-alpha, or TGF-beta were assessed by immunohistochemistry, while the expression of the differentiation marker carcinoembryonic antigen (CEA) was assessed on Western blots. Over the course of 6 d, static 3D cultures displayed the highest rates of proliferation and lowest apoptosis. This was associated with high EGF-R, TGF-alpha, and TGF-beta expression which was greater than that of a monolayer culture. Both rotated 3D lg and 3D microg cultures displayed lower expression of EGF-R, TGF-alpha, or TGF-beta and proliferation than that of monolayer or static 3D cultures. However, rotated 3D microg displayed significantly less apoptosis and greater CEA expression than rotated 3D 1g cultures. When rotated cultures of MIP-101 cells were grown uncler static conditions for another 3 d, proliferation increased and apoptosis decreased. Thus, rotation appears to increase apoptosis and decrease proliferation, whereas static 3D cultures in either unit or microgravity have less apoptosis, and reduced rotation in microgravity increases CEA expression.

Effect of low-dose oral contraceptives on androgenic markers and acne

Oral contraceptives (OC) suppress excess androgen production; however, different progestins in combination with low-dose estrogens produce divergent effects on sex hormone-binding globulin (SHBG) and testosterone that may influence clinical outcomes. This multicenter, open-label, randomized study compared biochemical androgen profiles and clinical outcomes associated with two OC containing the same amounts of ethinyl estradiol (EE, 20 micrograms) but different progestins, levonorgestrel (LNG, 100 micrograms), and norethindrone acetate (NETA, 1000 micrograms). Fifty-eight healthy women (18-28 years old) received three cycles of treatment with LNG/EE (n = 30) or NETA/EE (n = 28). The results showed that LNG reduced androgen levels in three compartments--adrenal, ovarian, and peripheral. NETA reduced only adrenal and peripheral androgens. Despite a 2.2-fold greater relative increase in SHBG with NETA than LNG, bioavailable testosterone (T) was reduced by the same amount with LNG and NETA. Both treatments improved acne and were well tolerated. Low-dose OC (EE, 20 micrograms) are effective in reducing circulating androgens and acne lesions without causing weight gain. Although LNG and NETA affected secondary markers differently, both OC formulations produced an equivalent decrease in bioavailable.

Reverse Micelle Formation Using a Sodium Di(n-Octyl) Phosphinate Surfactant

Sodium di(n-octyl) phosphinate was synthesized, purified, and used as a surfactant to form reverse micelles in isooctane at (22 +/- 1) degrees C by the contact method, which yields a Winsor II system. Two cosurfactants were investigated: decanol and di(n-octyl) phosphinic acid, and the ionic strength of the aqueous phase was adjusted with sodium chloride. For both cosurfactants, a minimum mole ratio of cosurfactant to surfactant was required to form reverse micelles and solubilize an appreciable amount of water in the organic phase. The maximum water uptake was obtained at this minimum mole ratio. No water uptake was obtained above a maximum value of the mole ratio of cosurfactant to surfactant. The maximum mole ratio was about 1 for di(n-octyl) phosphinic acid independent of acid concentration. For n-decanol, the maximum mole ratio decreased from about 3 to about 1 as the alcohol concentration increased from 0.15 to 0.30 m. The maximum water uptake increased with increasing cosurfactant concentration. Copyright 1999 Academic Press.

Management of irregular uterine bleeding and spotting associated with Norplant

Norplant, a systemic contraceptive, has been used extensively throughout the world. A major problem for consumers utilizing Norplant has been irregular, unpredictable uterine bleeding or spotting. This study seeks to determine whether or not an appropriate treatment could be found that will reduce the incidence of spotting and bleeding. Both a pilot study and an interim report of a multi-center trial utilizing ethinyl estradiol 20 micrograms for 10 days, versus Ibuprofen 800 mg three times a day for 5 days, versus placebo is reported. Based on the interim analysis of the multi-center trial, there is a reduction in the mean number of spotting days with one of the three treatments compared to the other two treatments (p = 0.044). There was no difference in the number of bleeding days between treatment regimen. It appears from a review of the literature that both oestrogen, progesterone, and non-steriodal anti-inflammatory agents may reduce the number of bleeding days or inhibit acutely the bleeding in women utilizing Norplant. The completion of this randomized multi-center trial will hopefully give us further insight into an effective treatment for controlling the irregular bleeding and/or spotting that occurs in Norplant users.

Left infrarenal region: anatomic variants, pathologic conditions, and diagnostic pitfalls

Computed tomography (CT) is the preferred method for evaluating the left periaortic infrarenal region. Structures larger than 11 mm in cross-sectional diameter in this region are considered abnormal and should be evaluated for lymphadenopathy, hydroureter, or a vascular abnormality such as venous thrombosis or varicoceles. Normal structures include inferior mesenteric vessels, left gonadal vein and artery, and ureter. The diagnostic process may be complicated by variations in anatomy, including double inferior vena cava, left inferior vena cava, retroaortic left renal vein, circumaortic left renal vein, horseshoe kidney, crossed-fused renal ectopia, renal agenesis, and ureteral duplication. Familiarity with the anatomy of this region and awareness of normal variants are necessary to avoid errors in diagnosis. Radiologists should also be aware of problems in CT technique (nonopacified bowel, dynamic and unenhanced scanning) that can confuse the diagnosis.

Effect of large palpable ovarian follicles on response to prostaglandin administration in dairy cows with corpora lutea

We examined the response to exogenous prostaglandin F2alpha in cattle with or without palpable structures believed to be ovarian follicles. All animals had ovarian structures diagnosed by palpation as corpora lutea. The cows were placed into two groups: those with follicles which were estimated by the palpators to be </=13 mm diameter (n=60); and cows with no palpable follicles or with follicles <13 mm diameter (n=133). Comparisons of proportion in estrus within five days, days to estrus, and milk progesterone levels failed to show significant differences between the groups.

Mucus transport by high-frequency nonsymmetrical oscillatory airflow

To study air-mucus interaction as a possible mechanism of tracheal mucus transport and to test the validity of using surface tracer displacement to indicate bulk mucus transport, we performed a combined experimental-theoretical study. We hypothesized that the mucus mass is moved by the difference between expiratory and inspiratory velocities. The rate of transport of a layer of simulated mucus lining the bottom of a rectangular trough was measured in two ways during oscillatory air flow. Peak velocity ratios (R) from 1.0 to 2.0, frequencies (f) between 7 and 13 Hz, and tidal volumes (VT) between 50 and 100 ml were generated by a custom-made pump. The experimental results demonstrate that measuring the displacement of a tracer deposited on the surface of the mucus layer is equivalent to measuring bulk mucus movement by weight. Moreover the measured mucus velocities (micron) correlate well with a theoretical model which predicts that micron is proportional to delta VT f1.5 (R-1). These results suggest that shearing at the air-mucus interface could be a significant factor in the enhanced tracheal mucus clearance during high-frequency chest wall oscillation.

Velocity profiles in central airways with endotracheal intubation: a model study

Steady inspiratory velocity profiles were measured at two flow rates in a 3:1 scale model of the human central airways in the presence of five modes of endotracheal intubation. The presence of an orifice or a short endotracheal tube had no significant effect on the velocity profiles distal to the carina. Long endotracheal tubes change the profiles in both main bronchi. A significant peak occurred in the frontal plane near the walls, and the maximum velocity in the airway was almost identical to the endotracheal tube center-line velocity. The flow impinging on the medial wall of the main bronchus was redirected up around the anterior and posterior walls yielding bipeak velocity profiles in the sagittal plane. A tube placed eccentrically in the trachea over the right main bronchus did not alter the velocity profiles in the left main bronchus, suggesting a redirection of flow over the carina into the left lung. An endobronchial tube at the mouth of the right main bronchus did change the shape of the velocity profiles in the left main bronchus. In the left upper lobar bronchus the presence of trachea intubation had no effect on the velocity profiles. However, in the right upper lobar bronchus, the long endotracheal tube flattened the velocity profiles from the strongly skewed ones seen in the absence of the endotracheal inserts. These results not only are relevant to distribution of ventilation and aerosol particle deposition, but also have strong implications in intrapulmonary gas mixing, especially when high-frequency low tidal-volume ventilation is involved.

Effect of the larynx on oscillatory flow in the central airways: a model study

Measurements were made of the effect of the larynx on the oscillatory flow profiles in a 3:1 scale model of the human central airways. A fixed glottic aperture corresponding to the shape and size at midinspiration was used. Oscillatory airflows at peak Reynolds numbers, similar to those obtained during spontaneous breathing and panting, were studied. The flow distribution to the five lobar bronchi was maintained by distally placed linear resistors. A hot-wire anemometer probe was used to measure the local velocity along two perpendicular diameters at six stations distributed through the model. Near the proximal end of the trachea, the flat velocity profiles at the beginning of the flow cycle peaked at maximum flow because of the jet created by the glottic aperture. This peaked structure was conserved during the latter half of the inspiratory cycle. Close to the carina, the jet had almost dissipated and the entry conditions into the main bronchi corresponded to those in the absence of the laryngeal model. The effect of the glottic aperture on the mean velocity was not felt beyond the carina, and the characteristic skewed profiles seen in oscillatory flows, in the absence of the larynx, were present in the main and lobar bronchi.

The effect of surgical excision and grafting procedures on postburn lymphocyte suppression

Previous reports have stressed the immunosuppressive effects of major surgical procedures. In this study, 30 adult patients with a mean burn size of 42.8% TBSA and a mean age of 31.9 years underwent 78 surgical excision and grafting (E/G) procedures. The mean surface area excised was 2,373 cm2, with a mean blood transfusion requirement per E/G of 3,355 cc or 1.4 cc/cm2. The suppressive effect of burn serum was assayed in mixed lymphocyte cultures. Before E/G, burn serum caused a mean 42.2 +/- 3.3% suppression of normal lymphocyte blastogenesis; serum suppressive activity following E/G was reduced to 29.1 +/- 2.9% (p less than 0.005). The mean duration of improvement in lymphocyte function was 5.0 days. E/G procedures which achieved complete burn wound closure were more effective in restoring lymphocyte immunocompetence. E/G has a significant beneficial effect on restoring lymphocyte responsiveness in burn patients. Preliminary evidence suggests that this effect is related to blood transfusions.

Model study of flow dynamics in human central airways. Part III: Oscillatory velocity profiles

Measurements of oscillatory velocity were made in a 3:1 model of the human central airways. The model was built of acrylic plastic and mounted vertically. A reciprocating pump connected to the upper end of the model privided oscillatory flow frequencies of 0.25, 1, 2 and 4 Hz (equivalent to 2.25, 9, 18 and 36 Hz in the actual airways) and tidal volumes of 300, 500 and 1500 ml. A hot-wire anemometer probe was used to measure velocities along two perpendicular diameters and at six stations distributed through the model. The flow distribution through the five lobar bronchi was controlled by distally positioned linear resistors . The measurements indicate that the entry flow profile into the model during oscillatory flow was essentially flat. At low frequencies, the velocity profiles attained at peak flow rate resemble the profiles seen under steady flow conditions at the corresponding Reynolds number. In the frontal plant these profiles are asymmetric with a maximum in velocity directed towards the outer wall of the bend. In the sagittal plane the velocity profiles are symmetric and have the characteristic bi-peak (M-shaped) structure seen in the steady flows. However, as the frequency increases the velocity profiles throughout most branches tend to flatten except in the right upper lobar bronchus where the skewed velocity profiles persist even at the highest frequencies studied. As in steady flows the nature of the velocity profile is strongly influenced by the airway geometry. Furthermore, the peak velocity profiles resemble steady flow profiles at comparable Reynolds numbers up to a Womersley number of 16.

The effect of plasma exchange on lymphocyte suppression after burn

Circulating mediators have been implicated in the pathophysiology of immunodepression after burn injury, suggesting the beneficial effect of plasma exchange in immunorestoration. In this study, 19 adult patients with a mean burn size of 52.2% of total body surface area and mean age of 33.4 years underwent 51 plasma exchange procedures in five different clinical settings, without complication. The suppressive effect of burn serum was assayed in mixed lymphocyte cultures. The mean (+/- SEM) suppression by burn serum drawn prior to plasma exchange was 61.9% +/- 3.6%, while that following plasma exchange was 27.3% +/- 2.7%. The lymphocyte response decrease 55.1% +/- 4.4% in suppressive activity. The mean duration of improvement in lymphocyte function was 4.8 days. Plasma exchange has a significant beneficial effect in restoring lymphocyte immunocompetence in burned patients in a number of clinical settings.

Resistance of mucus-lined tubes to steady and oscillatory airflow

We examined the effects of quantity and physical properties of mucus on resistance to steady and oscillatory flows in a circular tube. Gels with similar rheological properties to canine tracheal mucus were prepared from hog gastric mucin or locust bean gum cross-linked with Na2B4O7. A horizontal straight tube (D 1.85 cm) was lined with these mucus simulants to depths ranging from 0.3 to 1.0 mm. The pressure difference over a 50-cm portion of the tube and the volumetric flow rate were determined simultaneously. Low-amplitude oscillatory flow were generated with a modified Harvard pump. For steady flow, the resistance at low Reynolds number (Re) increased with increasing gel depth only to the extent expected for simple constriction of the tube cross-sectional area. The same was true for oscillatory (0.25--6 Hz) flow resistance at low flow amplitude (corresponding to Re less than 4,000). No effect of gel cross-link density at low Re was observed. At high steady-flow rates, and for high-amplitude oscillatory flow, resistance increased beyond that predicted for simple constriction. Plots of friction factor (f) vs. Re showed a critical point (Recrit) of the order of 1.5 x 10(4), at which f increased sharply. Recrit, which corresponded to the onset of wave formation in the lining layer, was insensitive to changes in gel depth. However, gel cross-link density did affect the onset of wave formation: in oscillatory flow Recrit was shifted to higher Re, and the rise in f in steady flow was blunted with high degrees of cross-linking. The existence of Recrit and its association with wave formation are consistent with predictions based on two-phase flow theory.

Hydrodynamic features of pulmonary air embolism: a model study

To elucidate the hydrodynamic events during pulmonary air embolism, experiments were conducted in a branching-tube apparatus and in small vessels. It was found that, as long as there existed an elevation differential between the two branches of a bifurcation, the vast majority of air bubbles always entered the higher branch. This finding is explained in terms of buoyancy, shear forces, and liquid flow velocity and is consistent with the in vivo finding of increased blood perfusion in the dependent lung regions during air embolization (J. Appl. Physiol.: Respirat. Environ. Exercise Physiol. 51: 211-217, 1981). The pressures required to drive air bubbles through various small vessels were determined using three aqueous solutions of different surface tensions. Based on these measurements and a theoretical analysis, the diameter of air bubbles that could not pass through the pulmonary vessels was calculated to be 20-30 micrometers, agreeing well with a recent in vivo measurement (J. Appl. Physiol.: Respirat. Environ. Exercise Physiol. 47: 537-543, 1979).

Hemolytic-uremic syndrome with prolonged anuria

Total cessation of urine formation beyond 4 days with ultimate survival is a rare occurrence. A child with the hemolytic-uremic syndrome was anuric for 27 days and renal function improved. the metabolic effects of acute renal failure require careful control of water and electrolyte balance and, when indicated, peritoneal and/or hemodialysis until renal function returns.