Small multidrug resistance (SMR) transporters contribute to bacterial resistance by coupling the efflux of a wide range of toxic aromatic cations, some of which are commonly used as antibiotics and ...antiseptics, to proton influx. EmrE is a prototypical small multidrug resistance transporter comprising four transmembrane segments (M1–M4) that forms dimers. It was suggested recently that EmrE molecules in the dimer have different topologies, i.e. monomers have opposite orientations with respect to the membrane plane. A 3-D structure of EmrE acquired by electron cryo-microscopy (cryo-EM) at 7.5 Å resolution in the membrane plane showed that parts of the structure are related by quasi-symmetry. We used this symmetry relationship, combined with sequence conservation data, to assign the transmembrane segments in EmrE to the densities seen in the cryo-EM structure. A C
α model of the transmembrane region was constructed by considering the evolutionary conservation pattern of each helix. The model is validated by much of the biochemical data on EmrE with most of the positions that were identified as affecting substrate translocation being located around the substrate-binding cavity. A suggested mechanism for proton-coupled substrate translocation in small multidrug resistance antiporters provides a mechanistic rationale to the experimentally observed inverted topology.
Noninvasive functional assessment of systemic right ventricles (RV) in hypoplastic left heart syndrome (HLHS) is challenging. This study aimed to compare pediatric cardiologists' current noninvasive ...imaging practices to those reported in 2013. A web-based survey was distributed to pediatric cardiologists via various listservs which queried timing of echocardiograms during HLHS palliative stages and measurements of RV function. Demographics of 156 participants who completed the 2023 survey were similar to survey participants in 2013 (n = 222). Respondents were mostly male (62%), echocardiographers (48%), in university-based practice (67%) in North America (95%). Echocardiograms were predominantly obtained monthly during interstage I (41%), every 6 months during interstage II (56%), and every year post-Fontan (68%), which is consistent from 2013. Routine cardiac magnetic resonance imaging (cMRI) significantly increased in interstage II (8.2%, 17%) and post-Fontan (24%, 56%) populations, respectively. Qualitative assessment (41%), ejection fraction (EF) by 3D (20%), fractional area change (16%), and RV strain/strain rate (13%) were preferred methods for systolic assessment, whereas a plurality of respondents (41%) did not believe RV diastolic measurements were valid. The largest gap between currently obtained and desired measurements existed for EF by 3D (46.5% points) and RV strain/strain rate (44.5% points). No differences existed between imagers compared to non-imagers. Variability in evaluating HLHS patients continues among pediatric cardiologists compared to 10 years ago. Qualitative assessment remains the primary RV systolic functional evaluation. Providers do not rely on quantitative RV diastolic function assessments in HLHS patients. Use of cMRI is increasing for RV functional analysis.Noninvasive functional assessment of systemic right ventricles (RV) in hypoplastic left heart syndrome (HLHS) is challenging. This study aimed to compare pediatric cardiologists' current noninvasive imaging practices to those reported in 2013. A web-based survey was distributed to pediatric cardiologists via various listservs which queried timing of echocardiograms during HLHS palliative stages and measurements of RV function. Demographics of 156 participants who completed the 2023 survey were similar to survey participants in 2013 (n = 222). Respondents were mostly male (62%), echocardiographers (48%), in university-based practice (67%) in North America (95%). Echocardiograms were predominantly obtained monthly during interstage I (41%), every 6 months during interstage II (56%), and every year post-Fontan (68%), which is consistent from 2013. Routine cardiac magnetic resonance imaging (cMRI) significantly increased in interstage II (8.2%, 17%) and post-Fontan (24%, 56%) populations, respectively. Qualitative assessment (41%), ejection fraction (EF) by 3D (20%), fractional area change (16%), and RV strain/strain rate (13%) were preferred methods for systolic assessment, whereas a plurality of respondents (41%) did not believe RV diastolic measurements were valid. The largest gap between currently obtained and desired measurements existed for EF by 3D (46.5% points) and RV strain/strain rate (44.5% points). No differences existed between imagers compared to non-imagers. Variability in evaluating HLHS patients continues among pediatric cardiologists compared to 10 years ago. Qualitative assessment remains the primary RV systolic functional evaluation. Providers do not rely on quantitative RV diastolic function assessments in HLHS patients. Use of cMRI is increasing for RV functional analysis.
To conduct a systematic review and meta-analysis to evaluate the association of a peritoneal interposition flap (PIF) with lymphocele formation following robotic-assisted laparoscopic radical ...prostatectomy (RALP) with pelvic lymph node dissection.
We conducted a systematic search of MEDLINE, Embase, Web of Science, and the Cochrane Central Register of Controlled Trials through August 30, 2023, to identify randomized and nonrandomized studies comparing RALP with pelvic lymph node dissection with and without PIF. A random effects meta-analysis was then performed to evaluate the associations of PIF with 90-day postoperative outcomes.
Five randomized controlled trials (RCTs) and four observational studies, including a total of 2941 patients, were included. The use of PIF was associated with a reduced risk of 90-day symptomatic lymphocele formation after RALP when examining only RCTs (pooled odds ratios OR 0.44, 95% CI 0.28-0.69; I2 =3%) and both RCTs and observational studies (OR 0.35, 95% CI 0.22-0.56; I2 =17%). Similarly, use of PIF was associated with a reduced risk of 90-day any lymphocele formation (OR 0.40, 95% CI 0.28-0.56, I2 =39%). There were no statistically significant differences in postoperative complications between the two groups (OR 0.89; 95% CI 0.69-1.14; I2 =20%).
Use of the PIF is associated with an approximately 50% reduced risk of symptomatic and any lymphocele formation within 90-days of surgery, and it is not associated with an increase in postoperative complications.
•Among those diagnosed with bladder cancer, male, uninsured, and non-White patients were more likely to be diagnosed with high-risk disease, as well as patients from lower education level ...areas.•Among those with high-risk NMIBC, patients who were older, non-White, Hispanic, uninsured or insured with Medicaid were less likely to receive guideline recommended intravesical BCG, while those residing in rural and higher education level areas were more likely to receive BCG.•When examining non-guidelines based use of radiotherapy for HGT1 disease, older age, and VA/Military insurance were associated with radiotherapy use.
To evaluate the associations of socioeconomic characteristics with the management of non-muscle invasive bladder cancer (NMIBC).
We identified adult patients aged 18 to 89 years with Ta, T1, or Tis NMIBC in the NCDB. We then examined the associations of patient and socioeconomic characteristics with the guidelines-based management of high-risk NMIBC using multivariable logistic regression.
163,949 patients were included in the study cohort, including 64% with Ta, 32% with T1, and 4% with Tis disease. Among those diagnosed with bladder cancer, male (OR 1.24, 95%CI 1.21–1.27), uninsured (OR 1.10, 95%CI 1.01–1.19 vs. private), and non-White (OR 1.34, 95%CI 1.28–1.41 for Black; OR 1.10; 95%CI 1.03–1.18 for Other vs. White) patients were more likely to be diagnosed with high-risk disease, as well as patients from lower education level areas. Among those with high-risk NMIBC, patients who were older, non-White, Hispanic, uninsured or insured with Medicaid were less likely to receive guideline recommended intravesical BCG, while those residing in rural and higher education level areas were more likely to receive BCG. When examining non-guidelines based use of radiotherapy for HGT1 disease, older age (OR 1.06; 95% CI 1.04–1.07) and VA/Military insurance (OR 2.73; 95%CI 1.07, 6.98 vs. private) were associated with radiotherapy use.
There are strong disparities in the prevalence and management of high-risk NMIBC. These observations highlight important targets for future strategies to reduce such healthcare disparities and provide more equitable bladder cancer treatment to patients.
Plasmodium falciparum reticulocyte-binding protein homolog 5 (RH5) is a leading blood-stage malaria vaccine antigen target, currently in a phase 2b clinical trial as a full-length soluble ...protein/adjuvant vaccine candidate called RH5.1/Matrix-M. We identify that disordered regions of the full-length RH5 molecule induce non-growth inhibitory antibodies in human vaccinees and that a re-engineered and stabilized immunogen (including just the alpha-helical core of RH5) induces a qualitatively superior growth inhibitory antibody response in rats vaccinated with this protein formulated in Matrix-M adjuvant. In parallel, bioconjugation of this immunogen, termed “RH5.2,” to hepatitis B surface antigen virus-like particles (VLPs) using the “plug-and-display” SpyTag-SpyCatcher platform technology also enables superior quantitative antibody immunogenicity over soluble protein/adjuvant in vaccinated mice and rats. These studies identify a blood-stage malaria vaccine candidate that may improve upon the current leading soluble protein vaccine candidate RH5.1/Matrix-M. The RH5.2-VLP/Matrix-M vaccine candidate is now under evaluation in phase 1a/b clinical trials.
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•Inhibitory antibodies from RH5.1/AS01B vaccinees target the RH5 α-helical core•A truncated and thermostabilized RH5.2 immunogen induces more potent antibodies•Bioconjugation of RH5.2 to VLPs enhances antibody immunogenicity in rodents•RH5.2-VLP/Matrix-M induces highest functional antimalarial antibodies in rats
King et al. describe an improved blood-stage malaria vaccine candidate, RH5.2-VLP, that outperforms the current clinical lead, RH5.1/Matrix-M, in rats. They demonstrate improved qualitative growth inhibitory antibody responses following deletion of disordered regions of RH5 and report the highest antibody-mediated in vitro growth inhibitory activity in RH5.2-VLP/Matrix-M-immunized rats.
Aim: We explored the extent to which occupancy of butterflies within three biogeographic regions could be explained by vegetation structure and composition, topography and other environmental ...attributes; whether results were consistent among regions; and whether assumptions of closure were met with assemblage-level sampling designs. Location: Chesapeake Bay Lowlands (Virginia), central Great Basin (Nevada) and western Great Basin (Nevada and California) (all USA). Methods: We applied single-season occupancy models that either assumed closure or relaxed the closure assumption to data from 2013 and 2014 for 13-15 species in each region. Results: Maximum single-year estimates of detection probabilities ranged from 0.14 to 0.99, and single-year occupancy from 0.28 to 0.98. The assumption of closure was met for a maximum of 54% of the species in a given region and year. Detection probabilities of > 90% of the species in each region increased as the categorical abundance of nectar or mud increased. Measures of the dominance or abundance of deciduous woody species and structural heterogeneity were included in the greatest number of occupancy models for the Chesapeake Bay Lowlands, which may in part reflect the intensity of browsing by whitetailed deer (Odocoileus virginianus). Elevation and precipitation were prominent covariates in occupancy models for Great Basin butterflies. Main conclusions: Because occupancy models do not rely on captures or observations of multiple individuals in a population, they potentially can be applied to a relatively high proportion of the species in an assemblage. However, estimation of occupancy is complicated by taxonomic, temporal and spatial variation in phenology. In multiple, widely divergent ecosystems, all or some associations between covariates and detection probability or occupancy for at least one-third of the species could not be estimated, often because a given species rarely was detected at locations with relatively low or high values of a covariate. Despite their advantages, occupancy models may leave unexplained the environmental associations with the distributions of many species.
Motivation: Motion in transmembrane (TM) proteins plays an essential role in a variety of biological phenomena. Thus, developing an automated method for predicting and simulating motion in this class ...of proteins should result in an increased level of understanding of crucial physiological mechanisms. We have developed an algorithm for predicting and simulating motion in TM proteins of the α-helix bundle type. Our method employs probabilistic motion-planning techniques to suggest possible collision-free motion paths. The resulting paths are ranked according to the quality of the van der Waals interactions between the TM helices. Our algorithm considers a wide range of degrees of freedom (dofs) involved in the motion, including external and internal moves. However, in order to handle the vast dimensionality of the problem, we employ some constraints on these dofs in a way that is unlikely to rule out the native motion of the protein. Our algorithm simulates the motion, including all the dofs, and automatically produces a movie that demonstrates it. Results: Overexpression of the RTK ErbB2 was implicated in causing a variety of human cancers. Recently, a molecular mechanism for rotation-coupled activation of the receptor was suggested. We applied our algorithm to investigate the TM domain of this protein, and compared our results with this mechanism. A motion pathway that was similar to the proposed mechanism ranked first, and motions with partial overlap to this pathway followed in rank order. In addition, we conducted a negative-control computational-experiment using Glycophorin A. Our results confirmed the immobility of this TM protein, resulting in degenerate paths comprising native-like conformations. Supplementary information: Supplementary data are available at Contact:angela@post.tau.ac.il
Motivation: Transmembrane (TM) proteins that form α-helix bundles constitute approximately 50% of contemporary drug targets. Yet, it is difficult to determine their high-resolution (< 4 Å) ...structures. Some TM proteins yield more easily to structure determination using cryo electron microscopy (cryo-EM), though this technique most often results in lower resolution structures, precluding an unambiguous assignment of TM amino acid sequences to the helices seen in the structure. We present computational tools for assigning the TM segments in the protein's sequence to the helices seen in cryo-EM structures. Results: The method examines all feasible TM helix assignments and ranks each one based on a score function that was derived from loops in the structures of soluble α-helix bundles. A set of the most likely assignments is then suggested. We tested the method on eight TM chains of known structures, such as bacteriorhodopsin and the lactose permease. Our results indicate that many assignments can be rejected at the outset, since they involve the connection of pairs of remotely placed TM helices. The correct assignment received a high score, and was ranked highly among the remaining assignments. For example, in the lactose permease, which contains 12 TM helices, most of which are connected by short loops, only 12 out of 479 million assignments were found to be feasible, and the native one was ranked first. Availability: The program and the non-redundant set of protein structures used here are available at http://www.cs.tau.ac.il/~angela
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