Search

Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting preferred orientations on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.

BACKGROUND: Murine data suggest that the placenta downregulates ferroportin (FPN) when iron is limited to prioritize iron for its own needs. Human data on the impact of maternal and neonatal iron status on placental FPN expression are conflicting. OBJECTIVES: This study aimed to identify determinants of placental FPN protein abundance and to assess the utility of the placental iron deficiency index (PIDI) as a measure of maternal/fetal iron status in newborns at high risk for anemia. METHODS: Placental FPN protein abundance was measured by western blots in placentae collected from 133 neonates born to adolescents (17.4 ± 1.1 y) carrying singletons (delivery gestational age [GA]: 39.9 ± 1.3 wk) and from 130 neonates born to 65 females (30.4 ± 5.2 y) carrying multiples (delivery GA: 35.0 ± 2.8 wk). Placental FPN and the PIDI (FPN:transferrin receptor 1) were evaluated in relation to neonatal and maternal iron-related markers (hemoglobin [Hb], serum ferritin [SF], soluble transferrin receptor [sTfR], total body iron [TBI], hepcidin, erythropoietin [EPO], erythroferrone). RESULTS: FPN protein was detected in all placentae delivered between 25 and 42 wk GA. Placental FPN protein abundance was associated with neonatal iron and erythropoietic markers (EPO: β: 0.10; 95% confidence interval [CI]: 0.06, 0.35; sTfR: β: 0.20; 95% CI: 0.03, 0.18; hepcidin: β: -0.06; 95% CI: -0.13, -0.0003; all P < 0.05). Maternal sTfR was only indirectly associated with placental FPN, with neonatal sTfR as the mediator (β-indirect: 0.06; 95% CI; 0.03, 0.11; P = 0.003). The PIDI was associated with neonatal Hb (β: -0.02; 95% CI: -0.03, -0.003), EPO (β: 0.07; 95% CI: 0.01, 0.14), and sTfR (β: 0.13; 95% CI: 0.004, 0.3) and with maternal SF (β: 0.08, 95% CI: 0.02, 0.14), TBI (β: 0.02; 95% CI: 0.009, 0.04), EPO (β: -0.10; 95% CI: -0.19, -0.01), sTfR (β: -0.16: 95% CI: -0.27, -0.06), and hepcidin (β: 0.05; 95% CI: 0.002, 0.11) at delivery (all P < 0.05). CONCLUSIONS: Placental FPN abundance was positively associated with neonatal indicators of increased erythropoietic activity and poor iron status. The PIDI was associated with maternal and neonatal iron-related markers but in opposite directions. More data are needed from a lower-risk normative group of females to assess the generalizability of findings. These trials were registered at clinicaltrials.gov as NCT01019902 and NCT01582802.

Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

Abstract This manuscript proposes a dual-band dual-polarized 64-element phased array antenna (PAA) with suppressed higher order modes (HoMs). Each array element is a microstrip patch structure with complementary split ring resonator (CSRR) loading, allowing for simultaneous dual-band and dual-polarization performance at 3.45 GHz and 3.87 GHz. The proposed PAA exhibits impedance matching of $$\le - 20$$ ≤ - 20 dB at 3.45 GHz and 3.87 GHz while limiting the mutual coupling below $$- 19$$ - 19 dB between the adjacent elements at both the operating bands. The proposed design includes a plated through hole placed near the CSRR loading to suppress any higher-order modes (HOMs). Two antenna prototypes, without and with HOMs suppression techniques are fabricated and measured. In addition, we demonstrate the beam steering of the proposed PAA up to $$\pm 60^0$$ ± 60 0 using an off-the-shelf 6-bit phase shifter module. The proposed 64 -element array achieves a gain of 23 dBi, and shows a minimal steering loss of $$\simeq 3$$ ≃ 3 dB over the steering angle.

Pyoderma is a one of the most common dermatological condition frequently observed in small animal practice. The genus Staphylococcus is responsible for approximately 90% of pyoderma cases in dogs, caused by bacterial infection. The purpose of the present study was to investigate the prevalence of major coagulase positive Staphylococcus bacteria causing different types of canine pyoderma in dog breeds. The samples were collected from the clinical cases of canine pyoderma with varying grade from the different breeds of dogs for the molecular based detection of major coagulase-positive Staphylococcus species. Out of total bacterial isolates, majority of them were molecularly identified as Staphylococcus spp. by 16S rRNA gene. Of these Staphylococcus spp., most common isolated organism was S. pseudintermedius (80.82%) followed by S. schleiferi subsp. coagulans (8.22%) and aureus (2.74%), using Pse-nuc, Sch-nuc, and Au-nuc genes, respectively.

Background Mendelian randomization (MR) studies suggest a causal effect of iron status on cardiovascular disease (CVD) risk, but it is unknown if these associations are confounded by pleiotropic effects of the instrumental variables on CVD risk factors. We aimed to investigate the effect of iron status on CVD risk controlling for CVD risk factors. Methods and Results Iron biomarker instrumental variables (total iron‐binding capacity [n=208 422], transferrin saturation [n=198 516], serum iron [n=236 612], ferritin [n=257 953]) were selected from a European genome‐wide association study meta‐analysis. We performed 2‐sample univariate MR of each iron trait on CVD outcomes (all‐cause ischemic stroke, cardioembolic ischemic stroke, large‐artery ischemic stroke, small‐vessel ischemic stroke, and coronary heart disease) from MEGASTROKE (n=440 328) and CARDIoGRAMplusC4D (Coronary Artery Disease Genome Wide Replication and Meta‐Analysis Plus the Coronary Artery Disease Genetics) (n=183 305). We then implemented multivariate MR conditioning on 7 CVD risk factors from independent European samples to evaluate their potential confounding or mediating effects on the observed iron–CVD associations. With univariate MR analyses, we found higher genetically predicted iron status to be associated with a greater risk of cardioembolic ischemic stroke (transferrin saturation: odds ratio, 1.17 [95% CI, 1.03–1.33]; serum iron: odds ratio, 1.21 [95% CI, 1.02–1.44]; total iron‐binding capacity: odds ratio, 0.81 [95% CI, 0.69–0.94]). The detrimental effects of iron status on cardioembolic ischemic stroke risk remained unaffected when adjusting for CVD risk factors (all P0.05). Conclusions Higher iron status was associated with a greater risk of cardioembolic ischemic stroke independent of CVD risk factors, and this effect was partly mediated by diastolic blood pressure. These findings support a role of iron status as a modifiable risk factor for cardioembolic ischemic stroke.

Vision-based grasping of unknown objects in unstructured environments is a key challenge for autonomous robotic manipulation. A practical grasp synthesis system is required to generate a diverse set of 6-DoF grasps from which a task-relevant grasp can be executed. Although generative models are suitable for learning such complex data distributions, existing models have limitations in grasp quality, long training times, and a lack of flexibility for task-specific generation. In this work, we present GraspLDM, a modular generative framework for 6-DoF grasp synthesis that uses diffusion models as priors in the latent space of a VAE. GraspLDM learns a generative model of object-centric $SE(3)$ grasp poses conditioned on point clouds. GraspLDM’s architecture enables us to train task-specific models efficiently by only re-training a small denoising network in the low-dimensional latent space, as opposed to existing models that need expensive re-training. Our framework provides robust and scalable models on both full and partial point clouds. GraspLDM models trained with simulation data transfer well to the real world without any further fine-tuning. Our models provide an 80% success rate for 80 grasp attempts of diverse test objects across two real-world robotic setups.

Abstract Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting “preferred orientations” on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.

Given the global climate change and frequent episodes of high temperature, globally legume crops including chickpea are receiving serious challenge of yield loss across the globe. Therefore, to sustain chickpea production breeders exploiting existing germplasm resources which can withstand drastically happening and fluctuating abiotic stresses like terminal heat and draught. A wide range of genetic variability for various phenological traits and yield related traits were recorded in 71 chickpea genotypes during normal and late or terminal heat stress sown conditions. The analysis of variance for all the environments revealed highly significant differences among the mean square due to genotypes for all the characters. The range of variation was comparatively wider in late sown condition than in normal sown conditions. The differences between phenotypic and genotypic coefficient of variation (PCV and GCV) were not substantial. High heritability coupled with high/moderate genetic advance expressed as percentage of mean were exhibited by hundred seed weight, seed yield/plant, number of pods/plants, plant height, reproductive phase duration, number of primary branches/plant and days to 50 % flowering under normal as well as late planting. So, these traits can be used as selection indices to improve seed yield in high temperature sown condition as well as timely sown condition. The pooled analysis of variance over dates of sowing (environments) were computed following Eberhart and Russell (1966) model. Genotype x environment interactions was highly significant for most of the characters except no. of primary branches/plant when tested against error mean square. G x E (linear) component was significant and higher than non-linear component for days to 50 % flowering, days to maturity, number of pods/plants, hundred seed weight and seed yield per plant. From the present study, five genotypes viz., ICC 14778, GJG 6, ICC 6579, ICC 8950 and ICC 10945 were highly stable for seed yield across the environments.

Research has already demonstrated the impact of positive and negative social interactions on one's self-efficacy. In particular, empowering or degrading messages from school teachers may have a significant long-term effect on students' self- efficacy. This is especially pertinent to students with ADHD symptoms, since they face increased challenges during childhood in school environment. The goals of the present study are to examine the relationships between memories of adults with ADHD and their social support and self-efficacy. 319 participants (253 (79.3%) females) reported their positive and negative memories of 'good' and 'bad' teachers, as well as current levels of perceived social support, ADHD symptoms' severity and self-efficacy. Results indicated a serial mediation model, in which the positive and negative memories, family support and peer support mediated the relations between ADHD symptoms and self-efficacy. In addition, ADHD symptoms predicted fewer positive memories, and more negative memories, and social support mediated their relations with self-efficacy.

The study aimed to understand how changes in crystal's size affect the lattice parameters and crystal structure of Mg1-xNixO solid solution for six X values ranging from x = 0 to x = 1. Mg1-xNixO was synthesized via two different wet-chemical techniques: the sol-gel and the microwave hydrothermal method, both followed by calcination at different temperatures of 673, 873, 1073, 1273 and 1473 K. As annealing caused grain growth, the varied temperature range allowed to examine a wide range of grain sizes. The lattice parameters and x values were determined from XRD (X-ray diffraction) peak positions and intensities respectively. The grain size was evaluated by XRD line profile analysis and supported by SEM (scanning electron microscope) observations. At the temperatures of 673 and 873 K grain size was in the nanometric range and from 1073 K and above grain size was in the micrometric range. A non-monotonic lattice variation versus grain size was found for each concentration. When grain size decreased there was a slight contraction, however for grain size in the nanometric range there was a severe lattice expansion. Both lattice parameter changes were explained by two effects acting together: contraction due to surface stress and expansion due to weakening of the ionic bonding at nanocrystalline particles. In this current research study, the lattice parameter was mapped in two dimensions: concentration and grain size. The findings of this study provided valuable insights into the lattice variation in the MgO–NiO solid solution system.

Osteogenesis imperfecta (OI) is a genetically heterogenous disorder most often due to heterozygosity for mutations in the type I procollagen genes, COL1A1 or COL1A2. The disorder is characterized by bone fragility leading to increased fracture incidence and long-bone deformities. Although multiple mechanisms underlie OI, endoplasmic reticulum (ER) stress as a cellular response to defective collagen trafficking is emerging as a contributor to OI pathogenesis. Herein, we used 4-phenylbutiric acid (4-PBA), an established chemical chaperone, to determine if treatment of Aga2+/- mice, a model for moderately severe OI due to a Col1a1 structural mutation, could attenuate the phenotype. In vitro, Aga2+/- osteoblasts show increased protein kinase RNA-like endoplasmic reticulum kinase (PERK) activation protein levels, which improved upon treatment with 4-PBA. The in vivo data demonstrate that a postweaning 5-week 4-PBA treatment increased total body length and weight, decreased fracture incidence, increased femoral bone volume fraction (BV/TV), and increased cortical thickness. These findings were associated with in vivo evidence of decreased bone-derived protein levels of the ER stress markers binding immunoglobulin protein (BiP), CCAAT/-enhancer-binding protein homologous protein (CHOP), and activating transcription factor 4 (ATF4) as well as increased levels of the autophagosome marker light chain 3A/B (LC3A/B). Genetic ablation of CHOP in Aga2+/- mice resulted in increased severity of the Aga2+/- phenotype, suggesting that the reduction in CHOP observed in vitro after treatment is a consequence rather than a cause of reduced ER stress. These findings suggest the potential use of chemical chaperones as an adjunct treatment for forms of OI associated with ER stress. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

Abstract Background Because often introduced without proper validation studies, so-called “add-ons” to IVF have adversely affected in vitro fertilization (IVF) outcomes worldwide. All-freeze cycles (embryo banking, EB) with subsequently deferred thaw cycles are such an “add-on” and, because of greatly diverging reported outcomes, have become increasingly controversial. Based on “modeling” with selected patient populations, we in this study investigated whether reported outcome discrepancies may be the consequence of biased patient selection. Results In four distinct retrospective case control studies, we modeled in four cohort pairings how cryopreservation with subsequent thaw cycles affects outcomes differently in good-, average- and poor-prognosis patients: (i) 127 fresh vs. 193 frozen donor-recipient cycles to model best-prognosis patients; (ii) 741 autologous fresh non-donor IVF cycles vs. 217 autologous frozen non-donor IVF cycles to model average prognosis patients; (iii) 143 favorably selected autologous non-donor IVF cycles vs. the same 217 frozen autologous cycles non-donor to monitor good- vs. average-prognosis patients; and (iv) 598 average and poor-prognosis autologous non-donor cycles vs. the same 217 frozen autologous non-donor cycles to model poor vs. average prognosis patients. In best-prognosis patients, EB marginally improved IVF outcomes. In unselected patients, EB had no effects. In poor-prognosis patients, EB adversely affected IVF outcomes. Unexpectedly, the study also discovered independent-of-age-associated chromosomal abnormalities, a previously unreported effect of recipient age on miscarriage risk in donor-egg recipients. Conclusions In poor-prognosis patients, EB cycles should be considered contraindicated. In intermediate-prognosis patients EB does not appear to change outcomes, not warranting additional cost and time delays. Therefore, only good-prognosis patients are candidates for EB, though they will experience only marginal benefits that may not be cost-effective.

Summary Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the sub-millisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature-jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.